Novel mhc class ii restricted t cell epitopes from the cancer antigen, ny eso-1

ABSTRACT

The present invention discloses the identification and isolation of novel MHC class II epitopes derived from the cancer antigen, NY ESO-1. The novel MHC class II epitopes from NY-EsO-1 are recognized by CD4 +  T lymphocytes in an HLA class II restricted manner, in particular HLA-DR or HLA-DP restricted. The products of the gene are promising candidates for immunotherapeutic strategies for the prevention, treatment and diagnosis of patients with cancer.

FIELD OF THE INVENTION

The present invention relates to the area of cancer diagnostics andtherapeutics including a cancer vaccine. More specifically, theinvention relates to the isolation and purification of a novel human MHCclass II restricted T cell epitope derived from the cancer peptide, NYESO-1 and analogs thereof and DNA sequence encoding the MHC class IIrestricted T cell epitope or portion thereof. In particular, theinvention relates to HLA-DR and HLA-DP restricted T cell epitopes fromNY ESO-1. The invention further relates to methods of detecting,diagnosing and treating cancer and precancer in an individual.

BACKGROUND OF THE INVENTION

T cells play an important role in controlling tumor growth and mediatingtumor regression. To understand the molecular basis of T cell-mediatedantitumor immunity, a number of tumor antigens recognized by CD8⁺ Tcells have been identified in melanoma as well as in other types ofcancers (1-3). These studies have led to several clinical trials usingpeptides derived from the molecularly defined tumor antigens (4-7).Although the clinical trial using a modified peptide derived from gp100provided some evidence of therapeutic efficacy for the treatment ofpatients with metastatic melanoma (4), these studies mainly focused onthe use of CD8⁺ T cells. Increasing evidence from both human and animalstudies has indicated that optimal cancer vaccines require theparticipation of both CD4⁺ and CD8⁺ T cells (8, 9). Moreover,tumor-specific CD4⁺ T cells are required for generating protectiveimmunity against MHC class II-negative tumor cells (10, 11).Identification of such antigens is thus important for the development ofcancer vaccines as well as for our understanding of the mechanism bywhich CD4⁺ T cells regulate host immune responses.

Thus far, only a limited number of MHC class II-restricted tumorantigens have been identified. Several known MHC class I-restrictedtumor antigens such as tyrosinase, gp100 and MAGE-3 were demonstrated tocontain MHC class II-restricted epitopes recognized by CD4⁺ T cells(12-15). Recently, a genetic approach was developed to identify unknownMHC class II-restricted tumor antigens by using tumor-specific CD4⁺ Tcells (16). This has led to the identification of several mutated tumorantigens including CDC27, TPI and LDFP (16, 17). Among them, TPI is amutated antigen that was independently identified by a biochemicalapproach (18).

The NY-ESO-1 gene was previously identified by antibody screening (19),and was recently identified as an MHC class I-restricted tumor antigenas well (20, 21). High titers of antibodies against NY-ESO-1 were alsodetected from patients with cancer (22). The NY-ESO-1 cDNA encoded twogene products from two overlapping open reading frames (20). Because ofits strict tumor-specific expression pattern with the exception ofexpression in normal testis as well as its high frequency of expressionin many tumors including melanoma, breast, prostate, lung and othercancers (18, 20, 23), NY-ESO-1 is potentially an important immune targetfor the development of immunotherapies for a variety of cancer types(24).

Although both CTL and antibody immune responses against NY-ESO-1 weredemonstrated in patients with cancer, no MHC class II-restricted T cellepitopes in the NY-ESO-1 protein have been reported.

The present invention is the identification and isolation of novel MHCclass II restricted T cell epitopes from NY-ESO-1 which are recognizedby CD4⁺ T cells. The cancer epitopes of the invention are useful as animmunogen and vaccine to inhibit or prevent cancer in a mammal and as adiagnostic agent to detect cancer or precancer.

SUMMARY OF THE INVENTION

One object of the present invention is to provide a novel peptide andportions thereof recognized as a MHC class II restricted T cell epitopeby CD4⁺ T lymphocytes. The antigenic cancer peptides of the presentinvention are encoded within or by a portion of the NY ESO-1 (term usedinterchangeably herein with CAG-3) gene (SEQ ID NO:1) (Genbank AccessionNo. AF038567; 8:9), or variants or homologs thereof such as LAGE gene(Genbank Accession No. AJ223040, AJ223041, and AJ223093).

One aspect of the invention are MHC class II restricted T cell epitopesencoded by the NY-ESO-1 gene, or variants thereof, which are useful as acancer vaccine capable of eliciting CD4⁺ T lymphocytes which results inprotection of the recipient from development of cancer and protectionfrom metastasis. The present invention also relates to a method ofadministering the cancer vaccine in an effective amount to inhibit orprevent cancers or inhibit the growth of cells expressing the NY-ESO-1gene product.

One aspect of the invention are HLA-DR and HLA-DP restricted T cellepitopes encoded by the NY-ESO-1 gene, or variants and homologs thereof,which are useful as an immunogen and as a cancer vaccine capable ofeliciting CD4⁺ T lymphocytes and an anti-NY-ESO-1 antibody response andin turn offering protection and/or therapeutic benefits to the recipientfrom development of cancer and protection from metastasis. The presentinvention also relates to a method of administering the cancer vaccinein an effective amount to inhibit or prevent cancers, inhibit the growthof cells expressing the NY-ESO-1 gene product and inhibit metastasis.

Another aspect of the present invention is a pharmaceutical compositioncomprising an MHC class II restricted T cell epitope derived fromNY-ESO-1 or variant thereof alone or in combination with one or moreimmunostimulatory molecules. The pharmaceutical composition comprisingat least one NY-ESO-1 MHC class II restricted T cell epitope, orcombination of epitopes which stimulate NY-ESO-1 antigen specific CD4⁺T-cells to elicit an immunogenic response against tumors and cancers.The pharmaceutical composition may additionally comprise one or more MHCclass I restricted T cell epitopes derived from NY-ESO-1 for generationof CD8⁺ T lymphocytes. The NY-ESO-1 MHC class II restricted T cellepitope and the NY-ESO-1 MHC class I restricted T cell epitope may eachbe provided as a discrete epitope or linked together and may be providedin the form of multimers. The cancer epitope or variant thereof may beprovided as an immunogen or as a vaccine for prevention or treatment ofcancer. The pharmaceutical composition is useful in methods of treatingor preventing cancer in a mammal. In the method of treatment, thepharmaceutical composition is administered to the mammal in an amounteffective in preventing or inhibiting the cancer in the mammal.

Another aspect of the present invention is a pharmaceutical compositioncomprising an HLA-DR restricted and/or an HLA-DP restricted T cellepitope derived from NY-ESO-1 or variant thereof alone or in combinationwith one or more immunostimulatory molecules. The pharmaceuticalcomposition comprising at least one NY-ESO-1 HLA-DR restricted T cellepitope or at least one NY-ESO-1 HLA-DP restricted T cell epitope, orcombination of MHC class II restricted T cell epitopes which stimulateNY-ESO-1 antigen specific CD4⁺ T-cells to elicit an immunogenic responseagainst tumors and cancers. The pharmaceutical composition mayadditionally comprise one or more MHC class I restricted T cell epitopesderived from NY-ESO-1 for generation of CD8⁺ T lymphocytes. The NY-ESO-1HLA-DR restricted T cell epitope or NY-ESO-1 HLA-DP restricted T cellepitope and the NY-ESO-1 MHC class I restricted T cell epitope may eachbe provided as a discrete epitope or linked together. The cancer epitopeor variant thereof may be provided as an immunogen or as a vaccine forprevention or treatment of cancer. The pharmaceutical composition isuseful in methods of treating or preventing cancer in a mammal. In amethod of treatment, the pharmaceutical composition is administered tothe mammal in an amount effective in eliciting CD4⁺ T cell and/oranti-NY-ESO-1 antibody response for preventing or inhibiting cancer inthe mammal.

Another object of the present invention is a method of generating MHCclass II restricted T cell epitopes of NY-ESO-1 or variants thereof bytranslation of DNA sequence encoding same from a NY-ESO-1 gene, portionor homolog thereof.

Another object of the present invention is a method of generating HLA-DRrestricted T cell epitopes or HLA-DP restricted T cell epitopes of NYESO-1 or variants or derivatives thereof by translation of DNA sequenceencoding same from a NY-ESO-1 gene or portion or homolog thereof.

A further aspect of the invention is the isolated DNA or RNA sequencethat encodes at least one MHC class II restricted T cell epitope ofNY-ESO-1 or variant thereof, and complementary sequence thereof and theuse of the DNA or RNA sequence as vaccines and in methods of producingthe MHC class II restricted T cell epitopes of NY-ESO-1 or variantsthereof. The invention further provides oligonucleotides of the DNA orRNA sequence for use as probes, primers or antisense.

A further aspect of the invention is the isolated DNA or RNA sequencethat encodes HLA-DR restricted T cell epitopes, HLA-DP restricted T cellepitopes of NY-ESO-1 or variant and combinations thereof and the use ofthe DNA or RNA sequence in methods of producing the HLA-DR restricted Tcell epitopes, the HLA-DP restricted T cell epitopes of NY-ESO-1 orvariants and combinations thereof. The invention further providesoligonucleotides of the DNA or RNA sequence for use as probes, primersor antisense.

The present invention further provides vectors comprising nucleic acidsequences encoding at least one MHC class II restricted cell epitope ofNY-ESO-1 or variant thereof alone or in combination with a second DNAsequence encoding at least one immunostimulatory molecule.

The present invention further provides vectors comprising nucleic acidsequences encoding at least one HLA-DR restricted T cell epitope or atleast one HLA-DP restricted T cell epitope of NY-ESO-1 or variant orcombination thereof alone or in combination with a second DNA sequenceencoding at least one immunostimulatory molecule.

The invention also provides host cells transfected or transduced with avector comprising DNA sequence encoding at least one MHC class IIrestricted T cell epitope of NY-ESO-1 or variant thereof alone or incombination with a second DNA sequence encoding at least oneimmunostimulatory molecule. The vectors and host cells may serve asvaccines in which expression of the MHC class II restricted T cellepitope results in the stimulation of tumor antigen specific CD4⁺ Tlymphocytes in a mammal immunized with the vaccine.

The invention also provides host cells transfected or transduced with avector comprising DNA sequence encoding at least one HLA-DR restricted Tcell epitope or at least one HLA-DP restricted T cell epitope ofNY-ESO-1 or variant or combination thereof alone or in combination witha second DNA sequence encoding at least one immunostimulatory molecule.The vectors and host cells may serve as vaccines in which expression ofthe HLA-DR restricted T cell epitope and/or the HLA-DP restricted T cellepitope results in the stimulation of tumor antigen specific CD4⁺ Tlymphocytes in a mammal immunized with the vaccine.

The invention provides a method of diagnosis of cancer or precancer in amammal by detection of a MHC class II restricted T cell epitope ofNY-ESO-1 or variant thereof.

The invention provides a method of diagnosis of cancer or precancer in amammal by detection of an HLA-DR restricted T cell epitope and/or anHLA-DP restricted T cell epitope of NY-ESO-1 or variant thereof.

It is yet another object of the invention to provide a method fordiagnosing human preneoplastic and neoplastic cells and tissues. Inaccordance with the invention, the method comprises isolating cells,tissues or extracts thereof from a human and detecting the DNA sequence,RNA sequence or portion thereof encoding a MHC class II restricted Tcell epitope of NY-ESO-1 or variant thereof or detecting the epitope orvariant thereof expressed by the DNA sequence or RNA sequence, whereindetection of/or increase in the DNA sequence, RNA sequence or expressionproduct is indicative of preneoplasia and neoplasia.

It is still another object of the invention to provide a method fordiagnosing human preneoplastic and neoplastic cells and tissues. Inaccordance with the invention, the method comprises isolating cells,tissues or extracts thereof from a human and detecting the DNA sequence,RNA sequence or portion thereof encoding an HLA-DR restricted T cellepitope or HLA-DP restricted T cell epitope of NY-ESO-1 or variantthereof or detecting the epitope or variant or combination thereofexpressed by the DNA sequence or RNA sequence, wherein detection of/orincrease in the DNA sequence, RNA sequence or expression product isindicative of preneoplasia and neoplasia.

Another object of the invention is to provide a transgenic animal whichhas incorporated into its genome one or more copies of the DNA sequenceencoding at least one MHC class II restricted T cell epitope of NY-ESO-1or variant thereof. The incorporation of the DNA sequence results inexpression or overexpression of the epitope. Such transgenic animals areuseful for screening of therapeutic agents useful in treating cancer.

Still another object of the invention is to provide a transgenic animalwhich has incorporated into its genome one or more copies of the DNAsequence encoding at least one HLA-DR restricted T cell epitope, or atleast one HLA-DP restricted T cell epitope of NY-ESO-1 or variant orcombination thereof. The incorporation of the DNA sequence results inexpression or overexpression of the epitope. Such transgenic animals areuseful for screening of therapeutic agents useful in treating cancer.

Still another aspect of the invention are monoclonal, polyclonal andrecombinant antibodies reactive with the MHC class II restricted T cellepitope of NY-ESO-1 or variant thereof, for use as a therapeutic and indiagnostic and detection assays. The monoclonal and polyclonalantibodies may be provided in the form of a kit alone, or along withother reagents commonly used in diagnostic and detection assays.

Yet another aspect of the invention are monoclonal, polyclonal andrecombinant antibodies reactive with the HLA-DR restricted T cellepitope or HLA-DP restricted T cell epitope of NY-ESO-1, or reactivewith the HLA-DP epitope in combination with the HLA-DP molecule or reactwith the HLA-DR epitope in combination with the HLA-DR molecule, orvariant thereof, for use as a therapeutic and in diagnostic anddetection assays. The monoclonal and polyclonal antibodies may beprovided in the form of a kit alone, or along with other reagentscommonly used in diagnostic and detection assays.

BRIEF DESCRIPTION OF THE FIGURES

These and other objects, features, and many of the attendant advantagesof the invention will be better understood upon a reading of thefollowing detailed description when considered in connection with theaccompanying drawings wherein:

FIGS. 1A and 1B. Nucleotide and amino acid sequence of NY-ESO-1.Numbering of nucleotide sequence of NY-ESO-1 starts from the firstnucleotide in the 5′ untranslated region.

FIG. 2A-2C:2 (A) Purification of full-length NY-ESO-1 protein using aNi²⁺ chromatography column. SDS polyacrylamide gel showed the crudeextract from E. coli strain BL21(DE3) bearing pET28 vector (lane 1),pNY-ESO-(lane 2), the purified NY-ESO-1 protein (lane 3), bacterialextract encoding the truncated NY-ESO-1 (lane 4), and the purifiedtruncated NY-ESO-1 protein, ESO1-74 (lane 5). (2B) Western blot toconfirm the specificity of antibodies against NY-ESO-1. Sera at 1 to2000 dilution from two representative patients, one with (lanes 1, 2,and 3) and one without (lanes 4, 5, and 6) detectable NY-ESO-1antibodies by ELISA were used against bacterial extract encoding thevector only (lanes 1 and 4), encoding NY-ESO-1 (lanes 2 and 5), and thepurified NY-ESO-1 protein (lanes 3 and 6). (2C) Patient TE was among themelanoma patients who had antibodies against NY-ESO-1 protein. ELISA wasperformed using sera from 88 patients for the presence of antibodiesagainst NY-ESO-1 (BSA as control protein). Values of O.D. 450 at 1:25,1:250, and 1:2500 of sera dilutions were plotted. Sera from normaldonors were used as controls, and their mean OD value was also plotted(ND).

FIG. 3. Testing of putative NY-ESO-1 epitopes using HLA-DR4-Tg miceimmunized with NY-ESO-1 protein. Eight peptides based on the predictedbinding affinity to HLA-DR4 were used for in vitro sensitization oflymphocytes from immunized mice. Murine lymphocytes were tested forIFN-production against either medium alone, 1359EBV B (HLA DR4⁺) cellsalone or 1359EBV B cells pulsed with the peptide used for in vitrostimulation.

FIG. 4A-4E. Characterization of the TE4-1 CD4⁺ T cell line. (4A) TE4-1specifically recognized 1088 EBV B cells (HLA-DR⁺) pulsed with ESOp116-135 peptide or purified NY-ESO-1 protein, but not ESO1-74 proteinwhich lacked the putative epitope. (4B) HLA DR-restriction was requiredfor the recognition of NY-ESO-1 by TE4-1. Two overlapping peptides ESOp111-130 and p116-135 were recognized when pulsed onto 293IMDR cells.1×10⁵ target cells were co-cultured with 4×10⁴ TE4-1 cells overnightbefore GM-CSF secretion was measured. (4C) Recognition of 293IMDR pulsedwith ESO p116-135 peptide was specifically inhibited by the anti-HLA-DRantibody (HB55), but not by the anti-class I antibody (HB95). The amountof GM-CSF secreted by TE4-1 in the absence of antibodies was used as thereference, against which the percent GM-CSF release in the presence ofantibodies was calculated. Inhibition by the control (mouse IgG2a) andthe anti-MHC-class I antibodies (HB95) had little effect. CTL C3G1(courtesy of C. Macalli) was a gp100 specific CD8⁺ T cell line thatrecognized 624.38mel, and was used as a control for the activity of HB95(FIG. 4D). T3-80 was a CD4⁺ T cell line that recognized 1362mel and wasused as the control for the activity of HB55 (FIG. 4E).

FIG. 5. Recognition of tumor cells by the CD4⁺ T cell line TE4-1. Allmelanoma lines used as targets for TE4-1 were analyzed for theexpression of HLA-DR4 and NY-ESO-1 by FACS and RT-PCR, respectively.TE4-1 was able to recognize NY-ESO-1⁺ tumor lines constitutivelyexpressing the HLA-DR4 molecule (1359mel and F049mel). F050melexpressing DR1 and NY-ESO-1 was also recognized by T cells. There was noreactivity against control targets 526mel (DR4 positive and NY-ESO-1negative), 397mel, 624.38mel (DR negative and NY-ESO-1 positive), nor1300mel (DR1 positive and NY-ESO-1 weakly positive).

FIG. 6A-6B. Characterization of the NY-ESO-1 peptide epitope recognizedby TE4-1. (6A) Determination of the anchor positions for the HLADR-restricted NY-ESO-1 epitope. 1088 EBV B cells were pulsed with 20 Mof the indicated peptides. TE4-1 cells were cocultured with the targetcells for overnight before GM-CSF was measured. (6B) Peptide titrationexperiment using ESO p119-130. ESO p119-130 was chosen based on itsrecognition shown in FIG. 6 (A). ESO p119-130 diluted at the indicatedconcentrations were pulsed onto 1088 EBV B cells, which were used astargets for recognition by TE4-1. Recognition of a control peptide, ESOp91-110 was measured only at the highest concentration of 33 M.

FIGS. 7A and 7B. 7A. Recognition of NY-ESO-1 protein and ESO p116-135 byTE4-1 using DR1+EBVB as APC. NY-ESO-1 protein (5 μg/ml) and peptides (33μM) were pulsed onto 586EBV B(DR1+) cells and washed twice. TE4-1 Tcells were then added and cocultured overnight before GM-CSF wasassayed. FIG. 7B. 586EBV B pulsed with ESOp116-135 (33 μM) was used tostimulate TE4-1 with and without the blocking antibodies. IID95(anti-class I antibody), IIB55 (anti-DR antibody), and isotype controlantibodies were used.

FIG. 8A-C. Generation of CD4⁺ T cells from PBMC after in vitrostimulation with synthetic peptides. (FIG. 8A) Specific peptidereactivity was detected in multiple wells after three in vitrostimulations. A total of 24 wells each containing 2.5×10⁵ PBMC in a96-well plate were stimulated weekly for three weeks. Fifteen of 24wells showed marked growth and tested for specific activity. T cellsfrom each well were incubated with 1088 EBVB cells and 1088 EBVB cellspulsed with the ESO p161-180 peptide, respectively. GM-CSF release wasmeasured from supernatants. (FIG. 8B). TE4-2 T cells specificallyreacted with NY-ESO-1 peptides and protein. Overlapping peptides ESOp161-180 and ESO p156-175 were pulsed onto 1088 (DR4⁺) and 586 EBVB(DR1⁺) cells at 20 micro g/ml for 90 minutes. ESO p91-110 was used as anirrelevant peptide for pulsing. Purified NY-ESO-1 and ESO1-75 proteinswere pulsed overnight at 5 micro g/ml and 2 micro g/ml respectively tomaintain the same molar ratio. After three washes, TE4-2 T cells wereadded and incubated overnight. GM-CSF release was measured. (FIG. 8C). Apanel of EBVB cells pulsed with ESO p161-180 were used as targets forTE4-2 CD4⁺ T cells. These EBVB lines were known to express different HLADR and DQ alleles. Their HLA DP alleles were molecularly typed in thisstudy (Table 2).

FIG. 9A-9C. Blocking of T cell recognition of NY-ESO-1 epitopes by ananti-DP antibody. 1088 EBVB cells pulsed with 20 micro g/ml ESO p161-180peptide were used as target cells in the presence of different blockingantibodies. Specificity of antibodies used was as follows: anti-MHCclass I (HLA A, B, C) antibody (W6/32), anti-MHC class II (HLA DP, DQ,DR) antibody (IVA12), anti-HLA DP antibody (B4/21), anti-HLA DR antibody(L243), and anti-HLA DQ antibodies (mixture of Genox 3.53 (anti-DQw1)and IVD12 (anti-DQw3)). All antibodies were used at a finalconcentration of 20 micro g/ml each. (FIG. 9A) CK3H6 T cellsspecifically recognized gp100 p209-218 peptide in the context of HLA A2and was used as the specificity control for anti-MHC class I antibody(FIG. 9B). 1088 EBVB (A2⁺) pulsed with gp100 p209-218 peptide was usedas targets. A CD4⁺ T cell line (T3-80) recognized 1362mel in an HLA-DRrestricted fashion and was used as the specificity control for anti-MHCclass II and anti-DR antibodies (FIG. 9C).

FIG. 10A-10B. Recognition of tumor cells and 293CIITA/NY-ESO-1 by TE4-2CD4⁺ T cells. (FIG. 10A). TE4-2 recognized melanoma lines expressingboth NY-ESO-1 and DP4. Melanoma lines with known NY-ESO-1 expression (byRT-PCR) and HLA DP types (determined by RT-PCR and sequencing) were usedas targets. An overnight IFN-gamma treatment (500 units/ml) wasconducted for F026mel, 526mel, and 397mel to up-regulate their MHC classII expression in this experiment. TE4-2 T cells were co-cultured withtumor cells overnight before cytokine release was measured. (FIG. 10B).TE4-2 CD4⁺ T cell line recognized 293CIITA transfected with NY-ESO-1with or without the invariant chain (Ii) targeting sequence. Parental293 cells and 293CIITA cells were transfected with plasmid encodingNY-ESO-1 (pESO), Ii-NY-ESO-1 (pIi-ESO), or GFP (pGFP), respectively.TE4-2 T cells were co-cultured with the transfectants overnight beforecytokine release was assayed.

FIG. 11A-11C. Characterization of T cell epitopes recognized by TE4-2.(FIG. 11A). Determination of the anchor residues and minimal length ofthe NY-ESO-1 epitope for T cell recognition. Synthetic peptides withamino acid deletions at the N- or C-terminus were used to pulse 1088EBVB cells at 40 micro g/ml. EBVB cells were then thoroughly washed andused as target cells to stimulate TE4-2 T cells. Two separateexperiments were conducted and presented as the top and bottom panel inthis figure. (FIG. 11B). Determination of the minimal peptideconcentration required for T cell recognition. The ESO p157-170 peptidewas used to pulse 1088 EBVB cells at various concentrations. The peptidepulsed cells were then washed and used as targets to stimulate TE4-2line. A control peptide ESO p91-110 was used only at the highestconcentration, 33 micromoles. (FIG. 11C). Recognition of theDPB1*0401-restricted CD4⁺ T cell epitope by the NY-ESO-1 specific CD8⁺ Tcells. TE8-1 cell line was generated from PBMC of patient TE by in vitrostimulation with the ESO p157-167 peptide. L023 EBVB cells (HLA-A2⁺,DP4⁻) were pulsed with peptides covering the DPB1*0401 epitope region ina serum-free medium, washed, and used to stimulate TE8-1 T cells.

FIGS. 12A and 12B. Titration of peptides for recognition by TE4-2 CD4+ Tcells and TE8-1 CD8+ T cells. FIG. 12A. 586 EBVB cells (A2−, DP4+) wereused as antigen-presenting cells to pulse with indicated peptides atvarious concentrations. Cells were washed and then incubated with TE4-2CD4+ T cells before cytokine release was assayed. FIG. 12B. L023 EBVBcells (A2+, DP4−) were used as antigen-presenting cells to pulse withindicated peptides at various concentrations. Cells were washed and thenincubated with TE4-2 CD4+ T cells before cytokine release was assayed.

DETAILED DESCRIPTION OF THE INVENTION

The present invention encompasses cancer epitopes, portion, derivativesor variants thereof of NY-ESO-1 which are immunologically recognized byMHC class II restricted CD4⁺ T lymphocytes of the immune system. Thecancer epitopes of the present invention specifically causes ahumoral-mediated immune response by interaction with CD4⁺ T cells of theimmune system.

This interaction between the antigenic cancer epitope and the CD4⁺ Tcells causes the CD4⁻ T cells to respond against, and recruit othercells in the immune system in the prevention, elimination or reductionof cancer in a mammal, including humans.

The NY-ESO-1 MHC class II restricted T cell epitopes of the presentinvention form part of or are derived from, cancers including but notlimited to primary or metastatic melanoma, thymoma, lymphoma, sarcoma,lung cancer, liver cancer, non-Hodgkin's lymphoma, Hodgkins lymphoma,leukemias, uterine cancer, cervical cancer, bladder cancer, kidneycancer, head and neck cancer, neuroblastoma and adenocarcinomas such asbreast cancer, prostate cancer, ovarian cancer, pancreatic cancer,thyroid cancer and the like.

The term melanoma includes, but is not limited to, melanomas, metastaticmelanomas, melanomas derived from either melanocytes or melanocyterelated nevus cells, melanocarcinomas, melanoepitheliomas,melanosarcomas, melanoma in situ, superficial spreading melanoma,nodular melanoma, lentigo maligna melanoma, acral lentiginous melanoma,invasive melanoma or familial atypical mole and melanoma (FAM-M)syndrome.

Of particular interest are cancer epitopes or derivatives thereofrecognized by autologous CD4⁺ T lymphocytes in patients with cancer, inparticular melanoma. Of further interest are cancer epitopes orderivatives thereof recognized by MHC (or HLA) class II restricted CD4⁺T lymphocytes, in particular HLA-DR restricted T lymphocytes and/or HLADP restricted T lymphocytes. In one embodiment, the NY-ESO cancerepitope is recognized by CD4+ T lymphocytes in context of HLA-DRmolecule. In another embodiment, the NY-ESO cancer epitope is recognizedby CD4+ T lymphocytes in context of an HLA-DP molecule.

The “cancer epitope” of the present invention encompasses a portion orvariant portion of NY-ESO-1 protein that elicites MHC class IIrestricted T lymphocytes, such as HLA-DR restricted and HLA-DPrestricted T lymphocytes. Such lymphocytes may specifically react withthe full length NY-ESO-1 protein, the MHC class II restricted T cellepitope and with naturally processed antigen from tumor cells.

The MHC class II restricted T cell epitope of NY-ESO-1 of the presentinvention may vary in size from about 9 amino acids to about 30 aminoacids, preferably about 10 to about 15 amino acids in length.

In a particular embodiment, the MHC class II restricted T cell epitopeof NY-ESO-1 of the present invention is about 9 to 10 amino acids inlength.

In one embodiment, the MHC class II restricted T cell epitope ofNY-ESO-1 is a peptide of at least about 10 amino acids in length thatcomprises the amino acid sequence:

Xaa₁ KEFTVSXaa₂ (SEQ ID NO: 4) and variants or derivatives thereof. Theamino acid at Xaa₁ and Xaa₂ and the number of amino acids at thesepositions at the N-terminus and C-terminus may vary as long as theepitope retains its ability to bind to/and stimulate CD4⁺ T lymphocytes.The epitope may comprise about 10 to about 30 amino acids, preferablyless than 20 amino acids, more preferably about 10 to about 15 aminoacids.

In another embodiment of the present invention the MHC class IIrestricted T cell epitope of NY-ESO-1 may be represented by the formula:

Xaa₁ VLLKEFTVSGXaa₂ (SEQ ID NO: 5), wherein Xaa₁ is no amino acid or oneto about 10 naturally occurring amino acids, preferably one to about 5amino acids; and Xaa₂ is no amino acid or one to about seven amino acidsin length.

In another embodiment of the present invention, the MHC class IIrestricted T cell epitope of NY-ESO-1 comprises the amino acid sequence:

QDAPPLPVPG VLLKEFTVSGNILTIRL (SEQ ID NO: 6), or fragments, orderivatives thereof.

Also encompassed in the ambit of the invention are cancer peptides orportions thereof that share partial sequence homology with SEQ. ID NO:4, 5 or 6. By partial amino acid sequence homology is meant a peptidehaving at least 85% sequence homology with SEQ. ID NO: 4, 5 or 6preferably at least 95% sequence homology or greater and has thebiological function of stimulating NY-ESO-1 MHC class II restrictedspecific CD4⁺ T lymphocytes. Mammalian homologs are included in theambit of the invention including but not limited to primate and murinehomologs.

In one embodiment the MHC class II restricted T cell epitope of NY-ESO-1comprises the amino acid sequence:

APPLPVPGVLLKEFTVSGNILTIRL (SEQ ID NO: 7);

APPLPVPGVLLKEFTVS (SEQ ID NO: 8);

APPLPVPGVLLKEFTV (SEQ ID NO: 9);

LPVPGVLLKEFTVSG (SEQ ID NO: 10);

PVPGVLLKEFTVSG (SEQ ID NO: 11);

VPGVLLKEFTVSG (SEQ ID NO: 12):

PGVLLKEFTVSG (SEQ ID NO: 13);

GVLLKEFTVSG (SEQ ID NO: 14);

LLKEFTVSGNILTIR (SEQ ID NO: 15)

LKEFTVSGNILTIRL (SEQ ID NO: 16);

KEFTVSGNILTIRL (SEQ ID NO: 17);

LPVPGVLLKEFTVSGNILTI (SEQ ID NO: 18);

or variant or derivatives thereof.

In a preferred embodiment of the MHC class II restricted T cell epitopeof NY-ESO-1 comprises the amino acid sequence:

and variants or derivatives thereof.

Epitopes having substitutions within the above sequence are encompassedby the present invention. A substitution of a naturally occurring aminoacid may be at one or more anchor positions, provided the substitutedamino acid(s) results in equivalent or enhanced binding compared to SEQID NO: 19. It is predicted that the anchor positions of SEQ ID NO: 19are at position 1-Leu, position 4-Glu, position 6-Thr, and position7-Val. In one embodiment alanine is substituted for leucine at position1.

In another embodiment of the present invention the MHC class IIrestricted T cell epitope of NY-ESO-1 comprises the amino acid sequence:

DHRQLQLSIS SCLQQLSLLM (SEQ ID NO: 20), portion, variants and derivativesthereof. In one embodiment, the portion of SEQ ID NO: 20 comprises theamino acid sequence:

DHRQLQLSIS SCLQQLS (SEQ ID NO: 29);

DHRQLQLSIS SCLQ (SEQ ID NO: 30);

QLQLSIS SCLQQL (SEQ ID NO: 31) or variants and derivatives thereof.

In another embodiment of the present invention the MHC class IIrestricted T cell epitope of NY-ESO-1 comprises the amino acid sequence:

WITQCFLPVF LAQPPSGQRR (SEQ ID NO: 21) portion, variants and derivativesthereof. In one embodiment, the portion of SEQ ID NO: 21 comprises theamino acid sequence:

QCFLPVF LAQPPSGQRR (SEQ ID NO: 32);

LPVF LAQPPSGQRR (SEQ ID NO: 33);

CFLPVF LAQPPSGQ (SEQ ID NO: 34); or variants and derivatives thereof.

The NY-ESO-1 cancer epitopes and derivatives thereof are recognized byMHC class II restricted CD4⁺ T lymphocytes. The class II moleculesrecognized in combination with the NY-ESO-1 epitope includes but are notlimited to at least one HLA-DR, such as HLA-DR1, HLA-DR3, HLA-DR4 andother class II molecules which function due to degeneracy of class IIpeptide binding. In one embodiment, an HLA subtype recognized by thecancer peptides is the HLA-DR4 subtype. In another embodiment, theNY-ESO-1 cancer epitope binds HLA-DR1 and HLA-DR4.

In another embodiment, the epitope is an HLA-DP restricted T cellepitope of NY-ESO-1, comprising the general amino acid motif of:

Xaa₁I TQ Xaa₂FXaa₃P Xaa₄ (SEQ ID NO: 51), wherein Xaa₁ is at least onenaturally occurring amino acid; preferably an amino acid selected fromthe group consisting of Trp, Phe, Tyr, Met, Ile, Val, Ala; andcombinations thereof,

Xaa₂ is at least one naturally occurring amino acid, preferably an aminoacid selected from the group consisting of Cys, Ser, Val, Ala, Thr; andcombinations thereof,

Xaa₃ is at least one naturally occurring amino acid, preferably an aminoacid selected from the group consisting of Leu, Phe, Tyr, Met, Ile, Val,Ala; and combinations thereof, and

Xaa₄ is at least one naturally occurring amino acid, preferably an aminoacid selected from the group consisting of Val, Tyr, Ile, Ala, Leu, Proand combinations thereof.

Also encompassed in the ambit of the invention are cancer peptides orportions thereof that share partial sequence homology with SEQ. ID NO:51. By partial amino acid sequence homology is meant a peptide having atleast 85% sequence homology with SEQ. ID NO: 51 preferably at least 95%sequence homology or greater and has the biological function ofstimulating NY-ESO-1 MHC class II restricted specific CD4⁺ Tlymphocytes, preferably HLA-DP restricted T lymphocytes. Mammalianhomologs are included in the ambit of the invention including but notlimited to primate and murine homologs. Homologs also include peptideshaving sequence homology with SEQ ID NO: 51 which may be encoded by agene other than the NY-ESO-1 gene, such as the LAGE gene.

Epitopes having substitutions within the above sequence are encompassedby the present invention. A substitution of a naturally occurring aminoacid may be at one or more anchor positions, provided the substitutedamino acid(s) results in equivalent or enhanced binding compared to SEQID NO: 51. It is predicted that the anchor positions of SEQ ID NO: 51are at position 1, 7, and 9, i.e., the W, L, and V residues,respectively. Substitutions of these anchor residues can be but notlimited to F, Y, M, I, V, and A for the “W” residue; F, Y, M, V, I, andA for the “L” residue; and Y, I, A, L, and P for the “V” residue.Another substitution may involve the C residue as position 5 of SEQ IDNO: 1, which can be but not limited to residues S, V, A, and T.

In one embodiment, the MHC class II restricted T cell epitope ofNY-ESO-1 is a peptide of at least about 10 amino acids in length thatcomprises the amino acid sequence:

Xaa₁ WITQCFLPVFXaa₂ (SEQ ID NO: 52) and variants or derivatives thereof.Xaa₁ and Xaa₂ may be no amino acid or one or more of the same or avariety of naturally occurring amino acids. The number of amino acids atthese positions at the N-terminus and C-terminus may vary as long as theepitope retains its ability to bind to/and stimulate CD4⁺ T lymphocytes,in particular HLA-DP restricted CD4⁺ T lymphocytes. The epitope maycomprise about 10 to about 30 amino acids, preferably less than 20 aminoacids, more preferably about 10 to about 15 amino acids.

In one embodiment, the HLA-DP restricted T cell epitope of NY-ESO-1comprises the amino acid sequence:

-   -   151-SCLQQLSLLMWITQCFLPVFLAQPPSG-177 (SEQ. ID NO.53);    -   SLLMWITQCFLPVF (SEQ. ID NO.54);    -   LLMWITQCFLPVFL (SEQ. ID NO.55);    -   LMWITWCFLPVFLA (SEQ. ID NO.56);    -   MWITQCFLPVFLAQ (SEQ. ID NO.57);    -   WITQCFLPVFLAQP (SEQ. ID NO.58);    -   ITQCFLPVFLAQPP (SEQ. ID NO.59);    -   QQLSLLMWITQCFL (SEQ. ID NO.60);    -   QLSLLMWITQCFLP (SEQ. ID NO.61);    -   LSLLMWITQCFLPV (SEQ. ID NO.62); and derivatives thereof.

The NY-ESO-1 cancer epitopes and derivatives thereof are recognized byHLA-DP restricted CD4⁺ T lymphocytes, and derivatives thereof,preferably HLA-DP4 restricted CD4⁺ T lymphocytes. The class II moleculesrecognized in combination with the NY-ESO-1 epitope includes HLA-DP andclass II molecules which function due to degeneracy of class II peptidebinding. A preferred HLA subtype recognized by the cancer peptides isthe HLA-DPB1*0401-0402 allele and other alleles that may bind to thepeptides due to function degeneracy.

Another embodiment of the present invention encompasses derivatives andvariants of the MHC class II restricted T cell epitopes of NY-ESO-1having sufficient homology to the epitopes thereof to effectively act toelicite MHC class II restricted CD4⁺ T lymphocytes. Such peptides mayhave conservative amino acid changes at one or more positions, inparticular in the anchor positions. By conservative amino acid changesis meant, an amino acid change at a particular position which is of thesame type as originally present; i.e. a hydrophobic amino acid exchangedfor a hydrophobic amino acid, a basic amino acid for a basic amino acid,etc. Such amino acid changes do not significantly alter the overallcharge and configuration of the peptide and therefore such variantsmaintain or enhance the anti-cancer activity of a cancer peptide.Examples of such conservative changes are well-known to the skilledartisan and are within the scope of the present invention.

The present invention also relates to functionally equivalent variantsof the NY-ESO-1 MHC class II restricted T cell epitopes. “Functionallyequivalent variants” includes peptides with partial sequence homology,peptides having one or more specific conservative and/ornon-conservative amino acid changes, peptide conjugates, chimericproteins, fusion proteins and peptides.

Another aspect of the invention are NY-ESO-1 peptides that function asepitopes for both HLA-DP restricted T cells and HLA class I restrictedCD8⁺ T lymphocytes, in particular for HLA-A restricted T lymphocytes,preferably HLA-A2 restricted T lymphocytes. In one embodiment, theHLA-DP restricted and HLA class I restricted epitope of NY-ESO-1comprise the amino acid sequence: SLLMWITQCFLPVF (SEQ ID NO: 54), aswell as variants and homologs thereof.

Variants include but are not limited to peptides having one or moresubstitutions in SLLMWITQCFLPVF (SEQ ID NO: 54) including but notlimited to ESOp156R-169 comprising: RSLLMWITQCFLPV (SEQ ID NO: 63) andESOp157-170R comprising: SLLMWITQCFLPVR (SEQ ID NO: 64). Suchsubstitutions render the peptide more soluble in aqueous solution whileretaining the immunologic functional activity of the native sequences.The highly water soluble peptides may be easily purified to more than90% purity.

The NY-ESO-1 MHC class II restricted T cell epitopes may be purified andisolated from natural sources such as from primary clinical isolates,cell lines and the like. The NY-ESO-1 MHC class II restricted T cellepitopes thereof are at least 90% pure, preferably at least 95% pure andas pure as 100%. The epitopes may also be obtained by chemical synthesisor by recombinant DNA techniques known in the arts. Techniques forchemical synthesis are described in J. M. Steward and J. D. Young,“Solid Phase Peptide Synthesis”, W.H. Freeman & Co., San Francisco,1969; M. Bodansky et al “Peptide Synthesis”, John Wiley & Sons, SecondEdition, 1976, and J. Meienhofer, “Hormonal Proteins and Peptides”, Vol.2, p. 46, Academic Press, New York, 1983 and E. Schroder and K. Kubke,“The Peptides”, Vol. 1, Academic Press, New York, 1965.

The NY-ESO-1 class II restricted T cell epitopes may be formulated withpharmaceutically acceptable carriers into pharmaceutical compositions bymethods known in the art. The composition is useful as an immunogen toelicit NY-ESO-1 specific CD4+ T lymphocytes and may be useful ineliciting anti-NY-ESO-1 antibody. The composition is also useful as avaccine to prevent or treat cancer. The composition may further compriseat least one immunostimulatory molecule. Immunostimulatory molecules tobe used in conjunction with the cancer epitope or portion thereof forstimulating MHC class II specific T cell responses include but are notlimited to one or more major histocompatibility complex (MHC) class IImolecules or cells expressing MHC class II molecules. The compositionmay further comprise other stimulator molecules including B7.1, B7.2,ICAM-1, ICAM-2, LFA-1, LFA-3, CD72 and the like, and cytokines whichinclude but are not limited to IL-1 through IL-15, TNFα, IFNγ, RANTES,G-CSF, M-CSF, IFNα, CTAP III, ENA-78, GRO, I-309, PF-4, IP-10, LD-78,MGSA, MIP-1α, MIP-1β, or combination thereof, and the like forimmunopotentiation.

The stimulatory molecule may be provided as a physically separate entityor it may be provided in the membrane of an antigen presenting cell suchas B-cell, macrophage or dendritic cell, in the membrane of a liposome,or expressed on the surface of a transduced or transfected cell. DNAsequences of MHC class II immunostimulatory molecules are available fromGenBank and the like. DNA sequences of HLA-DP immunostimulatorymolecules are available from the GenBank/EMBL/DNA Data Bank of Japan(DDBJ) at GenBank, National Center for Biotechnology Information, 8600Rockville Pike, Bethesda, Md. 20894 USA or from its web sites.

The pharmaceutical composition of the present invention may compriseseveral distinct MHC class II restricted T cell epitopes from NY-ESO-1in addition to the NY-ESO-1 HLA-DR or HLA-DP restricted T cell cancerpeptide thereof. These include but are not limited to the HLA-DRrestricted epitopes and variants thereof, such as LPVPGVLLKEFTVSG (SEQID NO: 10), VLLKEFTVSGNILTIRLT (SEQ ID NO: 65), AADHRQLQLSISSCLQQL (SEQID NO: 66), and combinations thereof.

The pharmaceutical composition of the present invention may optionallycomprise an MHC class I restricted NY-ESO-1 cancer peptide for elicitingMHC class I restricted cytotoxic T lymphocytes in addition to elicitingMHC class II restricted CD4⁺ T lymphocytes. MHC class I restrictedNY-ESO-1 cancer peptide include but are not limited to a cancer peptiderepresented by the formula:

Xaa₁ Xaa₂ Xaa₃ GP GGG AP Xaa₄ (SEQ ID NO: 22), wherein Xaa₁ is no aminoacid or one to about 20 naturally occurring amino acids, preferably oneto about 5 amino acids, Xaa₂ is Ala, Thr, Val, Leu or Arg, Xaa₃ is Seror a conservative substitution such as Ala, Val, Ile, Leu, Thr and thelike, Xaa₄ is Arg, Lys, preferably Arg, and fragments and derivativesthereof. In one embodiment, the MHC class I restricted NY-ESO-1 cancerpeptide for use in the pharmaceutical composition comprises the aminoacid sequence: ASGPGGGAPR (SEQ ID NO: 23).

The NY-ESO-1 MHC class H restricted T cell epitope and the NY-ESO-1 MHCclass I restricted T cell epitope may each be provided as a discreteepitope or linked together as a single peptide. The epitopes may belinked together or chemically synthesized by methods known in the art. Achemical linker, a peptide linker, a peptide bond and the like may beused for linking epitopes. In one embodiment, the C-temiinus of the MHCclass II epitope is directly linked to the N-terminus of the MHC class Iepitope via a peptide bond.

The NY-ESO-1 MHC class II restricted T cell epitopes are useful inmethods of preventing or treating cancer and useful in diagnostic assayfor detecting cancer or precancer in a mammal, including humans. In adiagnostic assay, the NY-ESO-1 HLA class II restricted T cell epitopepeptides, variants and derivatives thereof of the present invention areuseful in the detection of helper immune response against the tumorantigen, NY-ESO-1. Since NY-ESO-1 is exclusively expressed in tumorcells (except normal testis, which is an immune privileged site), theimmune response against the protein may be used as an indicator forearly cancer detection in patients. As the development of helper T cellresponses may be an earlier event than the development of detectableantibodies against the protein, detection of helper T cell responsesagainst the NY-ESO-1 HLA class II restricted T cell epitope peptides areuseful in early cancer detection. In a method of detecting helper Tcells responses to NY-ESO-1, NY-ESO-1 HLA class II restricted T cellepitope peptides are applied to a substrate or solid support.Lymphocytes from a patient are grown in the presence of the NY-ESO-1 MHCclass II restricted T cell epitope peptides in parallel with a controlpeptide such as a peptide from the flu virus. Specific cytokine releaseis then measured using such techniques such as ELISPOT and ELISA.Detection of an enhanced helper T cell immune response in comparison tothe negative controls is indicative of precancer or early cancer in thepatient.

The NY-ESO-1 MHC class II restricted binding peptides of the presentinvention may be used to enhance the generation of antibody and/or CD8+T cell responses against any given target antigen and/or hapten.Specifically, these peptides may be conjugated or covalently linked to atarget antigen peptide, protein or any other hapten against which anantibody and/or CD8+ T cell response is intended. The linkage of theNY-ESO-1 MHC class II restricted epitope peptide to any target hapten orprotein should act as a immunologic T cell carrier peptide in enhancingthe immunogenicity of any target antigen, hapten or protein in a mannersimilar to conventional T cell cancer proteins such as tetanus toxoid,albumin and the like. The enhancement may be manifest in higher titerantibody to the target hapten or protein, immunoglobulin class switchingform an IgM to an IgG or IgA antibody, and/or elicitation of CD8+ T cellresponses. Examples of such target antigen, hapten or protein includebut are not limited to TRP2, GP100, TRP1, gp120 and other HIV antigens,malaria antigens, epitopes thereof and the like. Similarly, the nucleicacid sequences encoding the NY-ESO-1 MHC class II restricted epitope maybe incorporated into an engineered vaccine construct along with anucleic acid sequence encoding a target antigen or epitope thereof forenhancement of the immunogenicity to the target antigen or epitopethereof. Examples regarding this aspect include to incorporate thenucleic acid sequence of Class II epitopes into any vaccine construct inthe form of naked DNA or RNA, vaccinia virus, adenovirus, fowlpox virusand the like in frame with the target gene. For example, to enhance theimmunogenicity of TRP2 antigen in the form of a plasmid vaccine, thenucleic acid sequence of the NY-ESO-1 class H epitope can be fused inthe same open reading frame with the TRP2 gene. The hybrid plasmid isthen used to immunize patients instead of using the plasmid encodingonly the TRP2.

The cancer epitopes or variants thereof may be in the form of aderivative in which other constituents are attached thereto such asradiolabels, biotin, fluorescein. A targeting agent may also be attachedto the epitope that allow for specific targeting to a specific organ,tumor or cell types. Such targeting agents may be hormones, cytokines,cellular receptors and the like. The epitope may be prepared in the formof a kit, alone or in combination with other reagents.

Another aspect of the invention is an immunogen or vaccine useful ininducing tumor-specific humoral-mediated immunity against cancer usingthe NY-ESO-1 MHC class II restricted epitopes of the present invention.The immunogen and vaccine elicit NY-ESO-1 specific CD4+ T lymphocytesand anti-NY-ESO-1 antibody. Optionally, the immunogen and vaccine maycomprise an NY-ESO-1 MHC class I restricted epitope for eliciting CD8⁺ Tlymphocytes.

Approaches to cancer immunotherapy can be divided into active or passivecategories. Active immunotherapy involves the direct immunization ofcancer patients with cancer antigens in an attempt to boost immuneresponses against the tumor. Passive immunotherapy refers to theadministration of immune reagents, such as immune cells or antibodieswith antitumor reactivity with the goal of directly mediating antitumorresponses.

Most prior attempts at active immunotherapy utilized either intactcancer cells or cancer cell extracts with the expectation that thesematerials contained tumor antigens in an amount and form capable ofstimulating immune responses. The molecular identification of cancerantigens and epitopes however, has open new possibilities for developingimmunotherapies for the treatment of human cancer. A summary of some ofthese approaches is presented in Table 1.

TABLE 1 Cancer Therapies Based on the Molecular Identification of CancerAntigens 1. Active immunotherapy with: a. Immunodominant peptides orepitopes 1) alone 2) combined with adjuvants 3) linked to helperpeptides, lipids or liposomes 4) pulsed onto antigen presenting cells b.Immunodominant peptides with amino acids substitutions to increasebinding to MHC molecules c. Proteins alone or combined with adjuvants d.“Naked” DNA encoding cancer antigens 1) “gene gun” for intradermalinjection 2) intramuscular injection 3) linked to lipids e. Recombinantviruses such as vaccinia, fowlpox or adenovirus encoding 1) cancerantigens or epitopes alone 2) cancer antigens or epitopes plus genesencoding cytokines, costimulatory molecules, or other genes to enhancethe immune response f. Recombinant bacteria such as BCG, Salmonella orListeria encoding cancer antigens alone or in combination withimmunostimulatory molecules 2. Active immunotherapy (above) followed bythe administration of immunostimulatory cytokines. 1. IL-2 2. IL-6 3.IL-10 4. IL-12 5. IL-15, and the like. 3. Passive immunotherapy withanti-tumor lymphocytes raised by in vitro sensitization of TIL or PBLto 1. immunodominant peptides pulsed onto antigen presenting cells(raise CD8⁺ cells) 2. antigenic proteins coincubated with antigenpresenting cells (exogenous antigen presenting pathway to raise CD4⁺cells).

The insertion of the gene encoding at least one NY-ESO-1 MHC class IIspecific T cell epitope into high efficiency expression systems such asE. coli, yeast or baculovirus and the like provides the opportunity toobtain large amounts of purified tumor epitopes for use in immunization.Alternatively, the immunodominant epitopes may be readily be synthesizedin vitro and purified in large amounts for immunization alone or in aform intended to improve their immunogenicity such as in combinationwith adjuvant, linkage to lipids/liposomes or helper peptides, or pulsedonto antigen presenting cells. Modification of individual amino acids ofthe immunodominant peptides to improve binding efficiency to MHC classII antigens can potentially increase immunogenicity compared to thenative peptide.

Recent techniques utilizing “naked” DNA injected directly into muscle orinto the skin have been shown to raise both cellular and humoral immunereactions to encoded antigens (Cooney, E. L., A. C. Collier, P. D.Greenberg, R. W. Coombs, J. Zarling, D. E. Arditti, M. C. Hoffman, S. L.Hu and L. Correy, 1991, Lancet 337:567; Wolff, J. A., R. W. Malone, P.Williams, W. Chong, G. Acsadi, A. Jani, and P. L. Feigner, 1990, Science247:1465; Davis, H. L., R. G. Whalen, and B. A. Demeniex, 1993, Hum.Gene Ther. 4:151; Yang, N. S., J. Burkholder, B. Roberts, B. Martinelli,and D. McCabe, 1990, Proc. Natl. Acad. Set. USA 87:9568; Williams, R.S., S. A. Johnston, M. Riedy, M. J. DeVit, S. G. McElligott, and J. C.Sanford, 1991, Proc. Natl. Acad. Sci. USA 88:2726; Fynan, E. R.,Webster, D. H. Fuller, J. R, Haynes, J. C. Santoro, and H. L. Robinson,1995, Proc. Natl. Acad. Sci. USA 90:11478; Eisenbraum, M. D., D. H.Fuller, and J. R. Haynes, 1993, DNA and Cell Bio. 12:791; Fuller, D. H.and J. R. Haynes, 1994, AIDS Res. Hum. Retrovir. 10(11):1433; Acsadi,G., G. Dickson, D. R. Love, A. Jani, F. S. Walsh, A. Gurusinghe, J. A.Wolff, and K. E. Davies, 1991, Nature 352:815). Techniques usingnonviable DNA vectors have the advantage of ease of preparation andsafety of administration. The nucleic acid sequence of the presentinvention is useful as an immunogen and as a DNA vaccine against cancer.The nucleic acid sequence of the present invention of the NY-ESO-1 MHCclass II specific T cell epitopes or a nucleic acid sequence encoding afull length NY-ESO-1 protein having one or more variant NY-ESO-1 MHCclass II restricted T cell epitopes thereof may be administered using agene gun in amounts to elicit a humoral response against a cancer cell.Nanogram quantities are useful for such purposes.

An effective form of immunization involves the incorporation of genesencoding immunogenic molecules into recombinant bacteria such as BCG,Salmonella or Listeria or into recombinant viruses such as vaccinea,fowlpox or adenovirus and the like. The genes encoding the NY-ESO-1 MHCclass II specific T cell epitope can be expressed either alone or incombination with genes encoding immunostimulatory molecules or othergenes which can enhance the immune response following infection. Theconstruct may additionally comprise a gene encoding an additionalNY-ESO-1 MHC class II restricted T cell epitope and/or at least oneNY-ESO-1 MHC class I specific T cell epitope. Studies with model tumorantigens in murine models have shown that incorporation of the gene forinterleukin-2 (IL-2) or B7.1 can increase the immunogenicity of modeltumor epitopes and even mediate the regression of established lungmetastases bearing these epitopes. Active immunotherapy followed by theexogenous administration of immunostimulatory cytokines such as IL-2,IL-6, IL-10, IL-12, or IL-15 may also be used to improve immuneresponses.

Passive immunotherapy with genetically modified immune cells (commonlyreferred to as adoptive immunotherapy) capable of recognizing humantumor antigens is effective in mediating the regression of cancer inselected patients with metastatic melanoma. In vitro techniques havebeen developed in which human lymphocytes are sensitized in vitro totumor antigen immunodominant epitopes presented on antigen presentingcells. By repetitive in vitro stimulation cells can be derived with afar greater capacity to recognize human tumor antigens than the TIL thatwere used to clone the genes encoding these antigens. Thus by repeatedin vitro sensitization with the cancer peptides, lymphocytes could bederived with 50 to 100 times more potency of TIL. The adoptive transferof these cells may be more effective in mediating tumor regression invivo than are conventionally grown TIL.

In one embodiment, peripheral blood mononuclear cells (PBMC) werestimulated with several candidate DRB1*0401 peptides identifiedfollowing immunization of DR4-IE transgenic mice. NY-ESO-1 specific CD4⁺T cells were generated by in vitro sensitization with a syntheticpeptide, ESO p161-180. This CD4⁺ T cell line recognized NY-ESO-1peptides presented by HLA DP4, a prevalent MHC class II allele presentin approximately 43-70% of Caucasians (52). Moreover, the HLA DP4haplotype was shared by 91% (10 out of 11) of the melanoma patients whoproduced high titer Ab against NY-ESO-1, but was not expressed in any ofthree patients with NY-ESO-1 positive tumors and possessing nodetectable Ab. The results of in vitro stimulation demonstrated that theHLA DP4-restricted T cells could be generated from 5 out of 6 patientswith NY-ESO-1 Ab. These results suggested that recognition of NY-ESO-1by CD4⁺ T cells in the context of DP4 could be connected with theability of these patients to mount an antibody response against thisantigen.

In the methods of preventing or inhibiting cancer, the NY-ESO-1 MHCclass H restricted T cell epitopes may be administered via one ofseveral routes including but not limited to intravenous, intramuscular,subcutaneous, intradermal, intraperitoneal, intrathecal, intrapleural,intrauterine, rectal, vaginal, topical, intratumor and the like.

Administration may be by transmucosal or transdermal means. Fortransmucosal or transdermal administration, penetrants appropriate tothe barrier to be permeated are used in the formulation. Such penetrantsare generally known in the art, and include, for example, fortransmucosal administration bile salts and fusidic acid derivatives. Inaddition, detergents may be used to facilitate permeation. Transmucosaladministration may be by nasal sprays, for example, or suppositories.For oral administration, the cancer peptide, tumor antigen, portion orvariant thereof is formulated into conventional oral administration formsuch as capsules, tablets and tonics.

In general, it is desirable to provide the recipient with a dosage ofNY-ESO-1 MHC class II restricted T cell epitopes of at least about 1 ngper Kg bodyweight, preferably at least about 1 mg per Kg bodyweight,more preferably at least about 10 mg or greater per Kg bodyweight of therecipient. A range of from about 1 mg per Kg bodyweight to about 100 mgper Kg bodyweight is preferred although a lower or higher dose may beadministered. The dose is effective to prime, stimulate and/or cause theclonal expansion of NY-ESO-1 MHC class II specific CD4⁺ T lymphocytes,which in turn are capable of preventing or inhibiting cancer in therecipient.

The dose is administered at least once and may be provided as a bolus ora continuous administration. Multiple administrations of the dose over aperiod of several weeks to months may be preferable. Subsequent dosesmay be administered as indicated.

In a method of treatment, a vaccine comprising the NY-ESO-1 class IIrestricted T cell epitope is administered to a mammal in an amounteffective to prevent cancer in the mammals or to prevent metastasis in amammal bearing a localized cancer. Optionally, the vaccine may includemultiple distinct NY-ESO-1 MHC class II restricted T cell epitopesand/or an NY-ESO-1 MHC class I restricted cancer peptide or epitope tostimulate cytotoxic T lymphocytes.

In a method of reducing tumor burden in animals having tumors the methodcomprises administration of an effective amount of a NY-ESO-1 MHC classII restricted T cell epitope at a site of tumor burden, said amount iseffective to reduce the size of the tumor at the site and may inhibitmetastasis from the tumor site.

In another embodiment of a method of treatment, an immunogen comprisingthe NY-ESO-1 HLA-DP restricted T cell epitope is administered to amammal in an amount effective to elicit NY-ESO-1 HLA-DP restricted CD4⁺T lymphocytes and anti-NY-ESO-1 antibody. The immunogen may be providedalone or in combination with an adjuvant, immunomodulators, and thelike.

In another method of treatment, autologous lymphocytes or tumorinfiltrating lymphocytes may be obtained from a patient with cancer. Thelymphocytes are grown in culture and cancer epitope specific CD4⁺lymphocytes expanded by culturing in the presence of NY-ESO-1 MHC classII restricted T cell epitopes alone or in combination with at least oneimmunostimulatory molecule with cytokines. The epitope specific CD4⁺lymphocytes are then infused back into the patient, alone or incombination with the epitope, in an amount effective to reduce oreliminate the tumors in the patient.

After immunization the efficacy of the vaccine can be assessed byproduction of immune cells that recognize the NY-ESO-1 MHC class II Tcell epitope, as assessed by antibody titer, specific lytic activity,specific cytokine production, tumor regression or combination of these.If the mammal to be immunized is already afflicted with cancer ormetastasis cancer the vaccine can be administered in conjunction withother therapeutic treatments such as immunomodulators, for example,IL-2, IL-6, IL-10, IL-12, IL-15, interferon, tumor necrosis factor andthe like, chemotherapeutic drugs such as cisplatinum, antiviral such asgancyclovir, amphotericin B, antibiotics and the like.

Another aspect of the invention is a DNA sequence of the NY-ESO-1 geneencoding a MHC class II restricted T cell epitope thereof.

In one embodiment, the DNA sequence comprises a portion of SEQ. ID NO.:1 or 2 and functionally equivalent sequence variants thereof that encodea MHC class II restricted T cell epitope recognized by CD4⁺ Tlymphocytes. Also encompassed by the present invention are nucleic acidsequences complementary, as well as anticomplementary to the portion ofSEQ. ID NO: 1 or 2 encoding the MHC class II restricted T cell epitope.

In an embodiment, the DNA sequence encodes an MHC class II restricted Tcell epitope comprising at least one of SEQ ID NOS: 4 through 21 or29-34.

In another embodiment, the DNA sequence encoding an MHC class IIrestricted T cell epitope comprises:

CAG GAT GCC CCA CCG CTT CCC GTG

CCA GGG GTG CTT CTG AAG GAG TTC

ACT GTG TCC GGC AAC ATA CTG ACT

ATC CGA CTC (SEQ. ID NO: 24) or functional portion or variant thereof.

In another embodiment, the DNA sequence encoding an MHC class IIrestricted T cell epitope comprises:

AGA CCA CCG CCA ACT GCA GCT

CTC CAT CAG CTC CTG TCT CCA GCA

GCT TTC CCT GTT GAT (SEQ ID NO: 25) or functional portion or variantthereof.

In another embodiment, the DNA sequence comprises:

TGG ATC ACG CAG TGC TTT CTG CCC

GTG TTT TTG GCT CAG CCT CCC

TCA GGG CAG AGG CGC (SEQ ID NO: 26), or functional portion or variantthereof.

Another aspect of the invention is a DNA sequence of the NY-ESO-1 geneencoding a HLA-DP restricted CD4⁺ T cell epitope thereof.

In one embodiment, the DNA sequence comprises a nucleic acid sequenceencoding one or more SEQ. ID NOS.: 51 through 64 and functionallyequivalent sequence variants thereof that encode an HLA-DP restricted Tcell epitope recognized by CD4⁺ T lymphocytes. Also encompassed by thepresent invention are nucleic acid sequences complementary, as well asanticomplementary to the nucleic acid sequence encoding the HLA-DPrestricted T cell epitope.

Due to degeneracy in the generic code, variations in the DNA sequencewill result in translation of an equivalent NY-ESO-1 epitope. As aresult, substitutions are included in the ambit of the invention as longas the substitution results in expression of an NY-ESO-1 epitope that isrecognized by NY-ESO-1 cancer antigen HLA-class II restricted CD4⁺ Tcells.

All or part of an open reading frame DNA sequence from the NY-ESO-1 genemay be used as probes to identify and isolate the homologs of theNY-ESO-1 MHC class II restricted T cell epitope in other mammalianspecies. In one embodiment, a human cDNA sequence is used to screen amammalian cDNA library for a murine homolog nucleic acid sequence.Positive clones are selected and sequenced. Examples of tissue sourcesfrom which the cDNA library can be synthesized include but are notlimited to dermis, epidermis, solid tumors, melanomas, melanocytes, andthe like. One skilled in the art will understand the appropriatehybridization conditions to be used to detect the homologs. Conventionalmethods for nucleic acid hybridization construction of libraries andcloning techniques are described in Sambrook et al, (eds) (1989) in“Molecular Cloning. A Laboratory Manual” Cold Spring Harbor Press,Plainview, N.Y. and Ausubel et al (eds) in “Current Protocols inMolecular Biology” (1987), John Wiley and Sons, New York, N.Y.

Another aspect of the invention are nucleic acid probes for thedetection and quantification of RNA that transcribes the NY-ESO-1 MHCclass II restricted T cell epitopes of the present invention in biologicsamples isolated from a mammal with cancer. Alterations in the level ofRNA relative to a control RNA sample is useful in diagnosis andprognosis of the disease in the mammal.

In one embodiment, mRNA is derived from tissue of a patient suspected ofhaving cancer or precancer and compared with mRNA derived from a healthycontrol subject. A quantitative and/or qualitative increase of the mRNAencoding a NY-ESO-1 MHC class II restricted T cell epitope of thepresent invention in the patient, as compared to the control, isindicative of cancer or precancer in the patient. The mRNA may bedetected using oligonucleotide probes hybridizable with the mRNA.

Combinations of oligonucleotides pairs based on the sequence encodingthe NY-ESO-1 MHC class II restricted T cell epitopes of the presentinvention may be used as PCR primers to detect mRNA in biologicalsamples using the reverse transcriptase polymerase chain reaction(RT-PCR) process for amplifying selected RNA sequences. The presentinvention also encompasses in situ PCR and in situ RT-PCR for detectionof DNA and RNA encoding the NY-ESO-1 MHC class II restricted T cellepitopes. The technique is preferred when the copy number of a targetnucleic acid is very low, or when different forms of nucleic acids mustbe distinguished. The method is especially useful in detecting anddifferentiating precancer and cancer cells from normal cells.

The present invention also encompasses antisense oligonucleotides whichbind to certain complementary (‘sense’) regions on mRNA resulting ininhibition of synthesis of NY-ESO-1. Such antisense oligonucleotides aresingle stranded nucleic acid of about 12 to about 25 mononucleotides andare antisense to the sequence encoding the NY-ESO-1 MHC class IIrestricted T cell epitopes of the present invention. Such antisenseoligonucleotides may be made by methods known in the art as described byUhlmann, E. et al. Antisense oligonucleotides, structure and function ofIn: Molecular Biology and Biotechnology Ed. R. A. Meyers, VCHPublishers, Inc., New York, N.Y., 1995, pp. 38-44.

The present invention also encompasses a vector comprising the DNAsequence encoding at least one or more NY-ESO-1 MHC class II restrictedT cell epitopes. The vector may comprise a DNA sequence encoding a fulllength NY-ESO-1 protein having one or more variant NY-ESO-1 MHC class IIrestricted T cell epitopes. Optionally the vector may also comprise aDNA sequence encoding at least one immunostimulatory molecule. Thevector may also comprise a DNA sequence encoding at least one or moreNY-ESO-1 MHC class I restricted T cell epitopes. The vector may alsocontain a gene encoding green fluorescent protein for use in detectinglocalization of NY-ESO-1 MHC class II restricted T cell epitopes incells and tissues.

Eukaryotic expression vectors include but are not limited to retroviralvectors, vaccinia virus vectors, adenovirus vectors, herpes virusvectors, fowlpox virus vectors, baculovirus vectors, humanpapillomavirus vectors, equine encephalitis vectors, influenza virusvectors and the like.

The present invention encompasses novel recombinant virus expressing atleast one NY-ESO-1 MHC class II restricted T cell epitope encoded by anopen reading frame nucleic acid sequence of a gene, fragments orvariants thereof. The recombinant virus may also express at least oneimmunostimulatory molecule. The recombinant virus is capable ofeliciting or upregulating a humoral immune response in a mammal for thepurpose of preventing or treating cancer in the mammal, particularlyhumans.

A host cell infected with the recombinant virus expresses one or moreNY-ESO-1 MHC class II restricted T cell epitopes, alone or incombination with at least one immunostimulatory molecule. The host cellmay also be infected with a recombinant virus expressing an HLA class IImolecule.

Methods for constructing and expressing exogenous gene products fromrecombinant vaccinia virus vectors are disclosed by Perkus et al Science229:981-984, 1985, Kaufman et al Int. J. Cancer 48:900-907, 1991, MossScience 252:1662, 1991, Smith and Moss BioTechniques November/December,p. 306-312, 1984, and U.S. Pat. No. 4,738,846. Sutter and Moss (Proc.Nat'l Acad. Sci. U.S.A. 89:10847-10851, 1992) and Sutter et al (Virology1994) disclose the construction and use as a vector, the non-replicatingrecombinant Ankara virus (MVA, modified vaccinia Ankara) which may beused as a viral vector in the present invention. Baxby and Paoletti(Vaccine 10:8-9, 1992) disclose the construction and use as a vector, anon-replicating poxvirus, including canarypox virus, fowlpox virus andother avian species for use as a viral vector in the present invention.

The vectors of the present invention may be placed in an appropriatehost cell for the expression of the NY-ESO-1 MHC class II restricted Tcell epitope. Eukaryotic host cell lines include, but are not limited toCOS cells, CHO cells, Hela cells, NIH/3T3 cells, insect cells, antigenpresenting cells such as dendritic cells and the like. Optionally thehost cell may also express a stimulatory molecule. In the case where thehost cells express both the NY-ESO-1 MHC class II restricted T cellepitope in combination with at least one MHC (or HLA) class II molecule,it is preferable that a eukaryotic expression system be used to allowfor proper glycosylation. The expression of both the cancer epitope andthe immunostimulatory molecule by the host cell provides the necessaryMHC class II restricted peptide to specific T cells and the appropriatesignal to the T cell to aid in antigen recognition and proliferation orclonal expansion of antigen specific T cells. The overall result is anupregulation of the immune system. The upregulation of the immuneresponse is manifest by an increase in cancer antigen specific CD4⁺lymphocytes and other effector cells of humoral immunity for inhibitionof the growth of cancer or precancer cells.

The DNA may be inserted into the host cell by transfection,transduction, liposomes and the like by methods known in the art.(Sambrook et al, 1989, in: “Molecular Cloning A Laboratory Manual”, ColdSpring Harbor press, Plainview, N.Y.). For liposomes, cationic lipidsare preferred, for example, polycationic lipid,dimyristyloxypropyl-3-dimethyl-hydroxyethyl ammonium (DMRIE) complexedwith the neutral phospholipid dioleoyl phosphatidyl-ethanolamine (DOPE)as disclosed by Nabel, E. G. et al, 1992, Hum. Gene. Ther. 3:367-275;Nabel, G. J. et al, 1992, Hum. Gene Ther. 3:649-656; Stewart, M. J. etal 1992 Hum. Gene Ther. 3:399-410; Nabel, G. J. et al 1993 Proc. Natl.Acad. Sci. USA 90:11307-11311; and Harrison, G. S. et al 1995 BioTechniques 19:816-823.

The recombinant NY-ESO-1 MHC class II restricted T cell epitopesexpressed by the host cells may be purified from cell lysates or cellsupernatants by standard protein purification procedures known in theart. These include but are not limited to molecular sievechromatography, ion-exchange chromatography, isoelectric focusing, gelelectrophoresis, affinity chromatography, HPLC, reverse phase HPLC andthe like. (Ausubel et al, 1987, in Current Protocols in MolecularBiology, John Wiley and Sons, New York, N.Y.). Immunoaffinitychromatography may also be used for purification using anti-cancerprotein antibodies or antigen binding fragments thereof as describedherein, as the immunoaffinity agent.

The recombinant virus may also be used as a therapeutic or vaccine. Insuch uses it is desirable to provide the recipient with a dosage ofrecombinant virus in the range of from about 10⁵ to about 10¹⁰ plaqueforming units/mg mammal, although a lower or higher dose may beadministered.

The recombinant viral vector may be introduced into a mammal eitherprior to any evidence of cancer such as melanoma or to mediateregression of the disease in a mammal afflicted with a cancer such asmelanoma. Examples of methods for administering the viral vector intomammals include, but are not limited to, exposure of cells to therecombinant virus ex vivo, or injection of the recombinant virus intothe affected tissue or intravenous, subcutaneous, intradermal,intramuscular and the like administration of the virus. Alternatively,the recombinant viral vector or combination of recombinant viral vectorsmay be administered locally by direct injection into the cancerouslesion or topical application in a suitable pharmaceutically acceptablecarrier. The quantity of recombinant viral vector, carrying the nucleicacid sequence of interest is based on the titer of virus particles. Apreferred range for immunization is about 10⁵ to 10¹⁰ virus particlesper mammal, preferably a human.

The invention provides a transgenic animal which has incorporated intoits genome one or more copies of the DNA sequence encoding at least oneNY-ESO-1 MHC class II restricted T cell epitope. The general method ofproducing transgenic animals is described in Krimpenfort ct al U.S. Pat.No. 5,175,384, Leder et al U.S. Pat. No. 5,175,383, Wagner et al U.S.Pat. No. 5,175,385, Evans et al U.S. Pat. No. 4,870,009 and Berns U.S.Pat. No. 5,174,986. The incorporation of the gene results inoverexpression, altered expression or expression of multiple forms orvariants of the NY-ESO-1 MHC class II restricted T cell epitope. Theresulting transgenic animal are useful in studies of the development ofcancer or tumor antigen of the present invention. The animal model isuseful in screening vaccines and chemotherapeutic drugs for cancertreatment. The transgenic animal is also useful in studies of thedevelopment of cancer.

This invention further comprises an antibody or antigen binding portionthereof elicited by immunization with the NY-ESO-1 MHC class IIrestricted T cell epitope of the present invention. In the case wherethe NY-ESO-1 MHC class II restricted T cell epitope is comprised of onlya few amino acids, the epitope may be conjugated to a carrier protein inorder to elicit an antibody response. Carrier proteins such as KLH,tetanus toxoid, albumin and the like and methods of conjugation areknown in the art. The antibody has specificity for and reacts or bindswith the NY-ESO-1 MHC class II restricted T cell epitope of the presentinvention, as well as with the intact NY-ESO-1 protein, and naturallyprocessed forms of the NY-ESO-1 protein.

Exemplary antibody molecules are intact immunoglobulin molecules,substantially intact immunoglobulin molecules or these portions of animmunoglobulin molecule that contain the antigen binding site, includingthose portions of immunoglobulin molecules known in the art as F (ab), F(ab′), F (abl, humanized chimeric antibody, and F (v). Polyclonal ormonoclonal antibodies may be produced by methods known in the art.(Kohler and Milstein (1975) Nature 256, 495-497; Campbell “MonoclonalAntibody Technology, the Production and Characterization of Rodent andHuman Hybridomas” in Burdon et al (eds.) (1985) “Laboratory Techniquesin Biochemistry and Molecular Biology”, Vol. 13, Elsevier SciencePublishers, Amsterdam). The antibodies or antigen binding fragments mayalso be produced by genetic engineering. The technology for expressionof both heavy and light chain genes is the subject of the PCT patentapplications: publication number WO 901443, WO 9014424, Huse et al(1989) Science 246:1275-1281, and U.S. Pat. No. 4,946,778. Humanizedimmunoglobulins having one or more complementary determining regions andmethods of making the antibodies are disclosed in U.S. Pat. Nos.5,585,089 and 5,530,101.

In one embodiment, the antibodies of the invention are used inimmunoassays to detect NY-ESO-1 peptides or portions containing the MHCclass II restricted T cell epitope in biological samples. The antibodiesor antigen binding fragments thereof may be used to detect cancerpeptides in tissue biopsy samples from a mammal afflicted with cancer.Assessment of the NY-ESO-1 MHC class II restricted T cell epitope in adiseased tissue can be used to prognose the progression of the diseasein a mammal or may diagnose the efficacy of a treatment. The immunoassaymay be a radioimmunoassay, Western blot assay, immunofluorescent assay,enzyme immunoassay, chemiluminescent assay, immunohistochemical assayand the like and may be performed in vitro, in vivo or in situ. Standardtechniques known in the art for ELISA are described in “Methods inImmunodiagnosis”, 2nd Edition, Rose and Bigazzi, eds. John Wiley & Sons,1980; Campbell et al “Methods and Immunology”, W.A. Benjamin, Inc.,1964; and Oellerich, M. 1984, J. Clin. Chem. Clin. Biochem. 22:895-904.Conventional methods for immunohistochemistry are described in Harlowand Lane (eds) (1988) In “Antibodies A Laboratory Manual”, Cold SpringHarbor Press, Cold Spring Harbor, N.Y.; Ausbel et al (eds) (1987) InCurrent Protocols In Molecular Biology, John Wiley and Sons (New York,N.Y.). Biological samples appropriate for such detection assays includebut are not limited to cells, tissue biopsy, whole blood, plasma, serum,sputum, cerebrospinal fluid, pleural fluid, urine and the like.

The antibodies or antigen binding fragments of the present invention mayalso be used in immunotherapy. The antibodies or antigen bindingfragment thereof is provided to a mammal in an amount sufficient toprevent, lessen or attenuate the severity, extent or duration of thecancer.

All articles and patents referred to are incorporated herein byreference.

While the invention is described above in relation to certain specificembodiments, it will be understood that many variations are possible,and that alternative materials and reagents can be used withoutdeparting from the invention. In some cases such variations andsubstitutions may require some experimentation, but will only involveroutine testing.

The foregoing description of the specific embodiments will so fullyreveal the general nature of the invention and others can, by applyingcurrent knowledge, readily modify and/or adopt for various applicationssuch specific embodiments without departing from the generic concept,and therefore such adaptations and modifications are intended to becomprehended within the meaning and range of equivalents of thedisclosed embodiments.

Example 1 Materials and Methods

Purification and Analysis of Recombinant NY-ESO-1 Protein:

To construct a bacterial expression vector encoding the full-lengthNY-ESO-1 gene, we generated a PCR fragment by using a pair of primers,ESO-5p (5′ GCTCCGGACATATGCAGGCCG AAGGCCGGGG) (SEQ ID NO: 35) containingan NdeI site and ESO-3p (5′ AAGGGGCTCGAGGCT GGGCTTAGCGCCTCT) (SEQ ID NO:36) containing an XhoI site. After digestion with restriction enzymesand gel purification of the PCR product, a DNA fragment encodingNY-ESO-1 was fused to DNA encoding a poly-histidine peptide in frame inpET-28(+) (Novagen, Madison, Wis.). A similar strategy was also used toconstruct an expression vector for a truncated NY-ESO-1, ESO1-74, whichcontained only the first 74 amino acid residues. E. coli strainBL21(DE3) bearing the correct plasmid construct was grown at 37° C. tolog phase, then induced for protein production by addingisopropyl-d-thiogalactoside (IPTG) to a final concentration of 0.5 mMand shaking for 3 hours. Soluble fractions of bacterial extract wereobtained; and NY-ESO-1 was purified by Ni²⁺ affinity chromatography.SDS-PAGE analysis of the purified protein was performed as previouslyreported (25). The N terminal sequence of the purified protein wasdetermined by automatic Edman degradation.

Serum and PBMC:

Sera from patients with metastatic melanoma were stored at −80° C. Seraof normal donors were obtained from the Blood Bank at the ClinicalCenter of NIH. The MHC class II genotype of patient TE with metastaticmelanoma was HLA-DR1*0401, 1*1501. The patient was treated with thegp100:209-217(210M) peptide plus high does of IL-2, and experienced anobjective tumor regression.

Detection of Antibodies Against NY-ESO-1 Protein:

About 50 ng of purified NY-ESO-1 protein diluted in 50 l PBST(phosphate-buffered saline with 0.1% Tween 20) was adsorbed to each wellof a 96-well MaxiSorp plate (Nunc, Denmark) overnight at roomtemperature. Control plates were coated with 150 ng BSA/well. Plateswere blocked with 5% dry milk in PBST for at least 2 hours, washed, andwere loaded with 100 l of diluted serum samples. All serum samples werediluted at 1:25, 1:250, and 1:2500 with 3% dry milk in PBST. Each sampleat the three different dilutions was loaded onto NY-ESO-1-coated platesas well as BSA-coated plates. After one hour incubation at roomtemperature, plates were washed, and loaded with secondary antibody(goat antihuman IgG conjugated with horseradish peroxidase, Sigma Co.,St. Louis, Mo.) diluted with 1% dry milk in PBST. Plates were developedafter a 0.5-hour incubation, and absorbance at 450 nm was read by usingan ELISA reader (Dynatech, Chantilly, Va.). A positive reaction wasdefined as an O.D. value against NY-ESO-1 that exceeded the mean O.D.value plus 3 times standard derivations of normal donors at serumdilutions of both 1:25 and 1:250. Western blot was performed asdescribed (24) to confirm the specificity of the antibody in a fewrepresentative sera samples.

Cell Lines and Antibodies:

Melanoma lines F049 and F050 were early cultures of fine needle asparatesamples, provided by Adam Riker at the Surgery Branch of NCl. All othermelanoma lines and EBV B lines were generated and maintained in RPMI1640 (Life Technologies, Rockville, Md.) supplemented with 10% fetalcalf serum (Biofiuid, Inc., Gaithersburg, Md.). 293IMDR1 and 293IMDR4were genetically engineered to express human invariant chain, DMA, DMBand DR molecules, and were cultured in RPMI 1640 supplemented with 10%fetal calf serum (15). Culture medium for murine lymphocytes was RPMI1640 with 0.05 mM-mercaptoethanol, 5 CU/ml IL-2 plus 10% fetal calfserum provided by Hyclone Inc. (Logan, Utah). Medium used for human Tcell culture was RPMI 1640 with 0.05 mM-mercaptoethanol, 50 CU/ml IL-2plus 10% human AB serum provided by Sigma Co. (St. Louis, Mo.). Antibodyblocking experiments were performed as previously described (15).Hybridoma HB55 and HB95 were obtained from American Type of Cell Culture(ATCC, Manassas, Va.). Control antibody was purchased from PhaimingenInt. (San Diego, Calif.).

Transgenic Animals and Immunization Procedures:

HLA-DR4 transgenic (DR4-Tg) mice were murine class II-deficient, andexpressed HLA-DR-IE- and HLA-DR1*0401-IE-chimeric molecules (26).Founder mice were obtained through Paul Lehmann at Case Western ReserveUniversity. Mice were inbred and maintained at Biocon Inc. (Rockville,Md.). Female mice aged between 6 and 10 weeks were immunized with thefull-length recombinant NY-ESO-1 protein. About 50 microgram of purifiedprotein were emulsified in complete Freund's adjuvant (CFA), dividedevenly and given to each mouse via subcutaneous injection into rear footpads and the base of tail. Eleven days after the injection, mice weresacrificed and the bilateral hindlimb popliteal and the inguinal lymphnodes were harvested. Single cell suspensions were obtained from thelymph nodes of two immunized animals, and followed by in vitrostimulation.

Peptide Synthesis:

Synthetic peptides used in this study were made using a solid phasemethod on a peptide synthesizer (Gilson Co. Inc., Worthington, Ohio) atthe Surgery Brach of NCl. The purity of each peptide was evaluated bymass spectrometry (Bio-synthesis, Inc., Lewisville, Tex.).

In Vitro Sensitization (IVS) Procedure and Cytokine Release Assays:

Peptides at a final concentration of 10 M were mixed with 2.5×10⁵ mouselymphocytes for a week before cytokine release assays were conducted.For IVS of human PBMC, 2.5×10⁵ cells were pulsed with peptides at 10 Mconcentration and incubated in each well of a flat-bottomed 96-wellplate. After two in vitro stimulations, cells were tested againstvarious targets and supernatants were harvested for cytokine releaseassays. Rapid expansion and cloning of human T cells were performed asdescribed (20).

Peptide at a final concentration of 10 M or protein at a finalconcentration of 5 g/ml were pulsed onto target cells. After 4 hrincubation, cells were washed in serum-free RPMI medium, andapproximately 3×10⁴ target cells were incubated with the same number ofTE4-1 cells overnight, and cytokine release was measured using GM-CSFELISA kits (R&D Systems, Minneapolis, Minn.) for human or IFN-kits(Endogen, Inc. Woburn, Mass.) for mouse. Other cytokines such as humanIFN-, IL-10, TNF-, and IL-4 were measured using ELISA kits from EndogenInc. or R&D Systems according to the manufacturer's instructions.

Example 2 Recombinant NY-ESO-1 Protein and Detection of NY-ESO-1Reactive Antibody

NY-ESO-1 reactive antibodies and CTL have been reported in patients withcancer (19-22). It thus appeared that NY-ESO-1 specific CD4⁺ T cellsmight play a role in orchestrating the development of antibodies as wellas CTLs against the NY-ESO-1 antigen. However, no CD4⁺ T cell epitopesfrom NY-ESO-1 have been reported thus far. In order to identify MHCclass II-restricted CD4⁺ T cell epitopes, we began by purifying NY-ESO-1protein from a bacterial expression system as the starting material. Tofacilitate NY-ESO-1 expression and protein purification, a cDNA fragmentencoding NY-ESO-1 was fused to a polyhistidine tag in frame located atthe N-terminus in the pET28 expression vector and a high-levelproduction of recombinant protein was obtained. Several milligrams ofthe NY-ESO-1 protein were purified by using a Ni²⁺-charged affinitychromatography column. The purified protein showed an apparent molecularweight of approximately 26 kDa on an SDS polyacrylamide gel (FIG. 2A).To confirm the identity of the purified protein, N terminalmicrosequencing of protein was performed by automatic Edman degradation.All 25 amino acid residues obtained by Edman degradation matched thepredicted amino acid sequences (data not shown). A short version ofNY-ESO-1 containing the first 74 amino acid residues, ESO1-74, was alsopurified by the same approach (FIG. 2A).

To determine whether melanoma patients developed antibodies against theNY-ESO-1 protein, sera from 88 metastatic melanoma patients enrolled incancer vaccine treatment protocols in the Surgery Branch, NCI werescreened. Sera from 8 normal donors were used as controls for screening.Eleven of 88 patients (13%) were found to have high titers of antibodiesagainst NY-ESO-1 (FIG. 2C). This data was consistent with resultsobtained by other groups (22). To exclude the possibility that patients'sera reacted with a minor contaminant present in the purified NY-ESO-1protein, Western blot was performed using representative sera samples.FIG. 2B showed that the NY-ESO-1 reactive sera from a patient reactedonly with cell lysates from NY-ESO-1 expressing bacteria and thepurified NY-ESO-1 protein, but not with extracts from bacteriacontaining the control vector. Anon-reactive serum sample was alsotested (FIG. 2B, lanes 4, 5, 6).

Example 3 Identification of Putative MHC class II-Restricted Epitopesfrom HLA-DR4-Transgenic Mice

To identify CD4⁺ T cell epitopes, DR4-transgenic mice were immunized inthe tail base and rear foot pads with approximately 50 g of full-lengthNY-ESO-1 protein in CFA. Eleven days after the injection, single cellsuspensions obtained from bilateral hindlimb popliteal and inguinallymph nodes of two immunized mice were prepared and used for in vitrosensitization with synthetic peptides derived from the NY-ESO-1 proteinbased on the predicted peptide binding properties of the HLA-DR4molecules (27).

Eight high-binding peptides containing amino acid sequence segmentspredicted to bind to HLA-DR4 were used for the in vitro sensitizationexperiments. Six days after the initial in vitro sensitization, murinelymphocytes were tested for cytokine release against human HLA-DR4positive 1359EBV B cells alone and 1359EBV B pulsed with thecorresponding peptide used for stimulation. Three peptides wererecognized by murine T cells based on cytokine secretion from T cellswhile other 5 peptides showed no recognition (FIG. 3). The ESO p116-135showed the strongest activity among the positive peptides, suggestingthat this peptide might contain an epitope presented by the HLA-DR4molecule for T cell recognition. This peptide was thus chosen forfurther analysis.

Example 4 Generation of Human CD4⁺ T Cells Specific for NY-ESO-1

PBMCs from patient TE, who had high-titered antibodies against NY-ESO-1(FIG. 2C), were used for in vitro stimulation with the ESO p116-135peptide. After one week of in vitro stimulation, PBMC from patient TEshowed marked expansion. IL-2 was added in the second week ofstimulation. The cell line thus established was named TE4-1, whichcontinued growth for more than two weeks in the presence of 20 CU/mlIL-2. The TE4-1 T cells were 90% CD4⁺ T cells based on FACS analysis.TE4-1 contained Th1-type CD4⁺ T cells as they secreted GM-CSF, IFN- andTNF, but not IL-10 or IL-4 (data not shown). After depletion of a fewpercent of CD8 T cells, the purified population of CD4⁺ T cells stillretained its reactivity. Some T cell clones derived from TE4-1 cell linewere also shown to recognize the ESO p116-135 peptide (data not shown).TE4-1 recognized EBV B cells pulsed with the full-length NY-ESO-1protein as well as the ESO p116-135 peptide in the context of HLA-DR4,but not with the truncated NY-ESO-1 protein containing the first 74amino acids (FIG. 4A). The TE4-1 cell line was also reactivespecifically with DR4 positive-dendritic cells infected with adenovirusencoding NY-ESO-1, but not adenovirus encoding the green fluorescenceprotein (data not shown).

To test whether T cell recognition by TE4-1 was restricted by HLA-DR4,two overlapping peptides (ESO p116-135 and ESO p111-130) and a controlpeptide (ESO p91-110) were pulsed onto 293IMDR1 and 293IMDR4 cells inserum-free medium. Cells were washed and subsequently incubated withTE4-1 cells overnight. As shown in FIG. 4B, both peptide 116-135 andpeptide 111-130 were recognized by TE4-1 in the context of HLA-DR4.Interestingly, peptide 116-135 was also capable of stimulating cytokinesecretion from T cells when pulsed onto 293IMDR1 cells. No activity wasdetected with 293IMDR4 pulsed with the control ESO p91-110 peptide (FIG.4B). The recognition of ESO-pi 16-135-pulsed 293IMDR4 was completelyinhibited by an anti-HLA-DR antibody (HB55), but not by the control andanti-HLA-class I antibodies (HB95) (FIG. 4C). A gp100-specific CD8⁺ Tcell line (CTL-C3G1) and an HLA-DR1-restricted CD4⁺ T cell line (T3-80)were used as specificity controls for the antibody blocking.

Example 5 Recognition of Tumor Cells by TE4-1

Although peptide-specific CD4⁺ and CD8⁺ T cell activities can often begenerated against a putative tumor antigen, in many cases tumorreactivity could not be demonstrated due to either the low affinity ofthe T cells or the failure of presentation of naturally processedpeptides on the tumor cell surface (3). To test whether TE4-1 couldrecognize NY-ESO-1 epitopes naturally processed and presented by tumorcells, several melanoma lines were used as targets. The expression ofNY-ESO-1 in each line was determined by RT-PCR, while the expression ofHLA-DR alleles was determined by FACS analysis (data not shown). Asshown in FIG. 5, TE4-1 was capable of recognizing NY-ESO-1/HLA-DR4positive tumors (1359mel and F049mel), but failed to recognize tumorcell lines 397mel and 624.38mel (NY-ESO-1⁺/HLA-DR⁻), nor 526mel(NY-ESO-1⁻/HLA-DR⁴⁺). Interestingly, TE4-1 also recognized F050mel(DR1⁺/NY-ESO-1⁺), but did not recognize 1300mel expressing DR1 and a lowlevel of NY-ESO-1. One possible explanation is that CD4⁺ T cells mayrecognize the same peptide presented by different DR molecules. Therecognition of F049mel could be specifically blocked in the presence ofanti-HLA-DR antibody, but not the anti-MHC-class I antibody (data notshown). These studies suggested that the TE4-1 cell line recognized anaturally processed peptide on the tumor cell surface.

Example 6 Characterization of the NY-ESO-1 Epitope Recognized by TE4-1

Since the two reactive peptides shared 15 amino acids (LPVPGVLLKEFTVSG)(SEQ ID NO: 10), the minimal length of peptide was determined by testinga series of N- and C-terminal truncated peptides. Peptides were pulsedonto DR4⁺ 1088 EBV B cells and tested for their ability to stimulateTE4-1 cells. The Valine residue at position 128 was found to be criticalfor T cell recognition (FIG. 6A). The peptides with the N-terminaldeletions up to Leucine residue at position 123 did not affect T cellrecognition, but the peptide with further deletions partially lost itsability to stimulate T cells. The Leucine residue at position 123 may bea P1 anchor residue since the P1, P4, P6 and P7 residues contributed tothe peptide binding to MHC class II molecules. Further deletions arerequired to determine the critical residues for binding to MHC class IImolecules.

Based on the deletion experiments, we used a short version of peptideESO p119-130 to determine the binding affinity of the peptide recognizedby TE4-1. Peptides were pulsed onto 1088EBV B cells (HLA-DR4⁺) astargets at different peptide concentrations. As shown in FIG. 5B, no orlittle T cell activity was observed at 33 nM or lower concentrations ofthe ESO p119-130 peptide; high activities were detected at 0.33 Mpeptide concentration and the T cell activity did not reached a plateauat a 33 M peptide concentration. The control peptide was not recognizedby TE4-1 even at a 33 M peptide concentration.

Example 7

We have shown that T4-1 CD4+ T cell line recognize ESO p116-135 in thecontext of DR4 and maybe DR1 as well. Here it is shown that TE4-1 canrecognize not only the peptide but also the protein in the context ofHLA-DR1. The recognition is blocked by anti-DR antibodies (FIGS. 7A and7B). This result shows evidence that ESO p116-135 may be a promiscuouspeptide and can bind to DR4 as well as DR1. Thus, the applicablepopulation of this peptide vaccine is quite large.

Example 8 Materials and Methods for HLA-DP Studies Cell Lines, TissueCulture Reagents, and Antibodies Used in the Study

293CIITA is a cell line generated by transduction of 293 cells with aretrovirus encoding the MHC class II transactivator (53) (The retroviralplasmid is a courtesy of Dr. George Blanc at the University of SouthFlorida, Tampa, Fla.). All melanoma lines and EBVB lines were generatedand maintained in RPMI 1640 (Life Technologies, Rockville, Md.)supplemented with 10% fetal calf serum (Biofluid, Inc., Gaithersburg,Md.). Culture medium for lymphocytes was RPMI 1640 with 0.05 mMbeta-mercaptoethanol, 50 CU/ml IL-2 plus 10% human male AB serumprovided by Valley Biochemicals Inc. (Winchester, Va.). Antibodies usedin blocking assays were obtained from the following sources: W6/32 (HLAclass I) and L243 (HLA DR) were hybridoma supernatant purified byLoftstrand Labs Lt. (Gaithersburg, Md.); Antibody clones IVA12 (HLAclass II), B7/21 (HLA DP), Genox 3.53, and IVD12 (both HLA DQ) werepurchased from Beckton Dickinson Immunocytometry Systems (San Jose,Calif.).

Construction of Plasmids

The pESO plasmid was an expression vector containing the NY-ESO-1 cDNAdriven by a CMV promoter as described before (45). The pIi-ESO plasmidwas constructed by inserting an NheI and NotI-digested PCR product ofthe whole NY-ESO-1 cDNA into the pTi80 vector digested with the sameenzymes (54). The NY-ESO-1 cDNA was fused in frame with the first 80amino acid residues of invariant chain (Ii) leader sequence at its Nterminus. PCR primers used to amplify NY-ESO-1 were as follows: forwardprimer 5′ cattgctagcATG CAG GCC GAA GGC CGG GGC A3′ (SEQ. ID NO. 73)containing an NHeI site and the reverse primer 5′ aaggctacattGC GGC CGCTTA GCG CCT CTG CCC TGA G3′ (SEQ. ID NO. 74) containing an NotI site.

Peptides and Generation of CD4⁺ T Cells

Synthetic peptides used in this study were made using a solid phasemethod on a peptide synthesizer (Gilson Co. Inc., Worthington, Ohio) atthe Surgery Branch, National Cancer Institute, Bethesda, Md. Afterdeprotecting, the purity of each peptide was evaluated by massspectrometry (Bio-synthesis, Inc., Lewisville, Tex.). Synthetic peptideswere lyophilized and reconstituted in DMSO at 20 mg/ml and diluted tothe indicated concentrations.

The in vitro sensitization procedure was carried out as previouslydescribed (50). Briefly, approximately 2.5×10⁵ PBMC were plated in a96-well flat-bottom plate in the presence of 20 micro g/ml peptide. Ondays 7 and 14, 1×10⁵ non-irradiated PBMC were pulsed with 20 micro g/mlpeptide, washed twice, and added to each well, and IL-2 at 20 CU/ad wasadded on day 8, day 11, day 15, and day 18. On day 21, cells wereharvested and incubated with target cells overnight before thesupernatants were taken for cytokine release assays.

T cells from those wells with specific activities were pooled andexpanded using the OKT-3 rapid expansion method (55). After expansion,CD8⁺ T cells were depleted from cultures using magnetic beads selection(Dynal Inc, Lake Success, NY); and the cell lines were subsequentlyanalyzed for CD4⁺ and CD8⁺ expression by flow cytometry.

Cytokine Release Assays

To prepare protein or peptide pulsed targets, peptides were used at afinal concentration of 20 micro g/ml, and proteins were used at a finalconcentration of 10 micro mg/ml. Cells were washed in serum-free RPMImedium, pulsed at 37 C in the absence of serum for 4 hours, followed by2× washes. Unless specified, approximately 3×10⁴ target cells wereincubated with the same number of T cells for at least 16 hours before acytokine release assay was carried out. Cytokine secretion was measuredusing a GM-CSF ELISA kit (R&D Systems, Minneapolis, Minn.). Quantitationof the levels of human IL-4, TNF-alfa, and TGF-beta was carried outusing cytokine kits obtained from the R&D Systems; and an IFN-gammaELISA kit was purchased from Endogen Inc (Woburn, Mass.). Assays werecarried out according to the manufacturer's instruction.

Molecular Typing of HLA DP Molecules

Total RNA was obtained from EBVB cells, CD40 ligand-stimulated B cells,CD4⁺ T cells, or MHC class II positive melanoma lines for typing. TotalRNA was purified using an RNeasy kit (Qiagen, Germany), and between 100ng and 1 micro g of RNA was used for oligo dT-primed first strand cDNAsynthesis. One tenth of the cDNA product was used to carry out PCRamplification with the advantage PCR system from Clontech (Palo Alto,Calif.). The following primer pairs were used for HLA DP-A and DP BPCRDPA forward primer 5′ ATG CGC CCT GAA GAC AGA ATG T 3′ (SEQ. ID NO. 75),DPA reverse primer 5′ TCA CAG GGT CCC CTG GGC CCG GGG GA3′ (SEQ. ID NO.76), DPB forward primer 5′ ATG ATG GTT CTG CAG GTT TCT G3′ (SEQ. ID NO.77), and DPB reverse primer 5′ TTA TGC AGA TCC TCG TTG AAC TTT C3′ (SEQ.ID NO. 78). The PCR product was subsequently purified and sequencedusing the identical primers that were used to carry out the PCR. Anumber of patients appeared to be homozygous for the highly prevalentHLA DPB1*0401 gene product, as a single sequence was obtained from thePCR product. In the case of heterozygous patients, the PCR product wasfirst cloned into a pCR4 vector (Invitrogen, Carlsbad, Calif.) andsequenced using 5′ and 3′ primers complementary to the vector sequence.The final sequence was searched against the IMGT-HLA database to confirmthe HLA DP identity (http://www3.ebi.ac.uk/Services/imgt/hla).

Example 9 Generation of a CD4⁺ T Cell Line TE4-2 Against NY-ESO-1

Initial studies were carried out to identify NY-ESO-1 epitopesrestricted by the HLA DR4 alleles. Eight 20-mer peptides which containedpredicted 9-mer DR4 binding motifs were examined for recognition bylymphocytes from HLA-DR4-IE transgenic mice immunized with the NY-ESO-1recombinant protein and stimulated in vitro (50). Three 20-mer peptideswere found to be positive in these experiments. One of them wascharacterized as a promiscuous epitope of both DRB1*0401 and DRB1*0101(50). To further characterize two other peptides, ESO p161-180 and ESOp141-160, we used them to stimulate PBMC from a DRB1*0401 patient (TE)who had high titer antibodies as well as CD4⁻ and CD8⁺ T cells againstNY-ESO-1 (50). A total of 24 micro-culture wells were used for eachpeptide. After three rounds of weekly stimulation, 15 out of 24 wellsshowed marked growth from PBMC that were stimulated with ESO p161-180.Nine of the 15 growth positive wells tested showed specific cytokinerelease against peptide pulsed DRB1*0401-expressing 1088 EBVB cells(FIG. 8A). Specific CD4⁺ T cells were also generated from the PBMCstimulated with ESO p141-160, but were not discussed in this study (datanot shown).

T cells from cultures that specifically responded to the ESO p161-180peptide stimulation were then combined and expanded using a protocoldescribed previously (55). Following the depletion of CD8⁺ T cells, thisculture, designated TE4-2, contained greater than 95% CD4 T cells asassessed by FACS analysis (data not shown).

Analysis of the cytokine secretion profile of TE4-2 demonstrated thatthis T cell line secreted IFN-gamma, TNF-alfa, IL-4 and GM-CSF, but notTGF-beta in response to peptide pulsed targets (data not shown). Thus,both Th1 and Th2 types of CD4⁺ T cells may be present in this cell line.Alternatively, cells with a Th0 phenotype may be present in thisculture.

Example 10 Recognition of NY-ESO-1 by TE4-2 in the Context of HLADPB1*0401-0402

TE4-2 T cells was examined to respond to DR4 expressing target cellspulsed with ESO p161-180, an overlapping peptide, ESO p156-175, as wellas the full-length NY-ESO-1 protein, respectively. 586 EBVB cells, whichexpressed DR1 but not DR4, were also used as APC. An irrelevant peptide,ESO p91-110, and a purified truncated recombinant protein, ESO1-74,comprising amino acid 1-74 (50) were used as controls. TE4-2 T cellsspecifically recognized a DR4⁺1088 EBVB line, when pulsed with thefull-length NY-ESO-1 protein, but not the truncated ESO1-74 protein(FIG. 8B). Both the ESO p161-180 and p156-175 were recognized by TE4-2,indicating that the minimal peptide epitope resided between amino acid161 and 175. In contrast, the initially predicted DR4-binding motifresided between amino acid 167 and 175. Unexpectedly, the TE4-2 T cellline appeared to respond equally well to peptides and proteins pulsed on586 EBVB cells, which expressed DRB1*0101 but not DRB1*0401. This resultsuggested that either similar peptides were presented by multiple MHCclass II restriction elements, or 1088 and 586 EBVB cell lines shared anMHC class II restriction element that presented the peptides to TE4-2 Tcells. To test these possibilities, a number of other EBVB cells withknown HLA DR and DQ types were also used as APC in an attempt toidentify the restriction element utilized by TE4-2 T cells. All but oneof the EBVB cell lines tested were able to present the ESO p161-180peptide to TE4-2 (FIG. 8C).

T cell recognition of peptides was then carried out in the presence ofspecific antibodies that blocked the recognition of peptides restrictedby different MHC restriction elements. The results in FIG. 9A through 9Cdemonstrated that an antibody which blocked all MHC class II alleles(IVA12) and an antibody with a specificity for blocking all HLA DPalleles (B4/21), abolished the ability of TE4-2 T cells to recognize ESOp161-180. Antibodies directed against HLA-A, B, and C alleles (W6/32) aswell as antibodies against the MHC class II DR (L243) and DQ (a mix ofGenox 3.53 and IVD12) alleles, had little or no effect on thestimulation of TE4-2 T cells. Thus, these results suggested that theTE4-2 T cells recognized ESO p161-180 in the context of a highlyprevalent HLA DP allele shared by EBVB cell lines used in this study.

The HLA-DP alleles were then molecularly cloned and sequenced for celllines used in FIG. 8C. These studies showed that 1088 and 586 EBVB lineswere both homozygous for the HLA DPB1*0401 gene product, and patient TEexpressed DPB1*0401 as well as an unknown DP allele (Table 2). L023 EBVBcell line, which did not present the ESO p161-180 peptide to TE4-2 wastyped as homozygous for the HLA DP allele, which was distinct fromDPB1*0401 and 0402. The 1363, 1088, 836, and L007 EBVB cell lines allexpressed DPB1*0401, whereas L041 EBVB cell line expressed DPB1*0402,which was different from the DPB1*0401 molecule by two amino acidresidues at position 84 and 85. Thus, it appeared that both theDPB1*0401 and DPB1*0402 were able to present the ESO p161-180 epitope toTE4-2 CD4 T cells.

TABLE 2 HLA (DP, DQ, and DR alleles) typing of patients used in thisstudy. HLA-DP HLA-DQ HLA-DR Patients with NY-ESO-1 antibodies: TEB1*0401, nd 0302, 06** B1*0401, 1501; B4*0101, B5*0101 BE B1*0401 0301,0302 B1*0401, 1102; B3*0202, B4*01** AC B1*04 negative 0603, 0604B1*1301, 1302; B3*0202, B3*0301 FJ B1*0401 0502, 0601 B1*1502, 1601;B5*0102, B5*02** LD B1*0401 0303, 0603 B1*0901, 1301; B3*0101, B4*01**CJ B1*0401, nd 0201, 0301 B1*0701, 1101; B3*0202, B4*01** BFE B1*0402,nd 0303, 0602 B1*0701, 1501; B4*01**, B5*0101 KF B1*0401, 0402 0301,0603 B1*0401, 1301 ; B3*0101, B4*0101 CT B1*0401, 0402 0301, 0603B1*1101, 1502; B3*0202, B5*0102 DA B1*0401 06** B1*08**, 15**; nd BLB1*0401, nd 0201, 0602 B1*0301, 1501; B3*0101, B3*0202 Patients withNY-ESO-1 expressing tumor but no detectable Ab: FS B1*04 negative 0301,0501 B1*0101, 1101; B3*0202 BFJ B1*04 negative 0201, 05** B1*0701, 1601;B3*0101, B3*0202 MJ B1*04 negative 0501 B1*1501; B5*0101 EBVB lines usedfor antigen presentation: L007 EBVB B1*0401 0602 B1*1501 B5*0101 L023EBVB B1*04 negative 0301 B1*1201 B3*0202 L041 EBVB B1*0402, nd 0402B1*0822 nd 836 EBVB B1*0401, nd 02** B1*0701; B4*01** 1363 EBVB B1*04010501 B1*0101; nd 1088 EBVB B1*0401 0201, 0301 B1*0301, 04**; B3*0101,B4*01** 586 EBVB B1*0401 0501, 0201 B1*0101, 07**; B4*01** “nd”: notdetermined. **subtypes unknown. The detection of the presence ofNY-ESO-1 antibodies in melanoma patients was previously described (50).To determine whether it required a specific DPA chain to present theepitope to TE4-2 T cells, the HLA DPA molecules in DPB1*0401-0402expressing EBVB cells were also analyzed. DPB1*0401-0402 expressing EBVBcells as used in FIG. 8C had more than one type of HLA DPA molecule(data not shown); however, all were able to present the NY-ESO-1 epitopeto TE4-2 T cells equally well.

Example 11 Recognition of a Naturally Processed NY-ESO-1 Epitope onTumor Cells by TE4-2

To investigate whether the T cell epitope recognized by TE4-2 wasnaturally processed and presented on the surface of tumor cells, tumorlines that expressed NY-ESO-1 as well as DPB1*0401 were used as targets.TE4-2 T cells recognized multiple tumor lines expressing both NY-ESO-1and DPB1*0401, but failed to recognize a tumor line that expressedNY-ESO-1, but did not express any of the HLA DPB1*0401 and 0402 alleles(1362mel) (FIG. 10A). In addition, TE4-2 T cells failed to recognizeDPB1*0401 negative and NY-ESO-1 negative tumors (526mel). One melanomaline, 1102mel, which expressed HLA DPB1*0401 but did not expressNY-ESO-1, was also recognized by TE4-2 T cells. The results of RT-PCRanalysis demonstrated that 1102mel expressed the LAGE-1 gene, acancer/testis antigen possessing approximately 90% amino acid similarityto NY-ESO-1 (57). A sequence identical to ESO p161-175 was also presentin the LAGE-1 protein. These results suggested that epitopes recognizedby TE4-2 were present on the surface of tumor cells, and that it isshared between NY-ESO-1 and the closely related tumor antigen LAGE-1.

In addition to NY-ESO-1 expressing melanoma lines, TE4-2 T cells werealso tested for recognition of NY-ESO-1 transfected 293CIITA cells.293CIITA cell line was generated by transducing 293 cells with aretrovirus expressing the MHC class II transactivator gene (CITTA) (53).The 293CIITA cells but not the parental 293 cells expressed homozygousHLA DPB1*0401 molecule as determined by RT-PCR (data not shown). TE4-2 Tcells reacted specifically with NY-ESO-1 transfected 293CIITA cells(FIG. 10B). In contrast, TE4-2 T cells failed to recognize either293CIITA cells transfected with the pGFP plasmid or parental 293 cellstransfected with Ii-NY-ESO-1. An Ii targeting sequence was not requiredfor the processing and recognition of NY-ESO-1, but slightly enhanced Tcell recognition (FIG. 10B). These results further demonstrated thatTE4-2 T cells recognized a naturally processed NY-ESO-1 epitope.

Example 12 HLA DP4-Restricted Epitopes Overlapping with an HLA-A2Restricted Epitope

Target cells pulsed with the two overlapping peptides, ESO p161-180 andp156-175 were recognized equally well by TE4-2 T cells, indicating thatthe minimal T cell epitope was located in the region ranging from aminoacids 161 to 175 (FIG. 8B).

In an attempt to identify the anchor residues present between amino acid161 and 175, a series of overlapping 13 mer peptides were used to pulse1088 EBVB cells and tested for their abilities to stimulate TE4-2 Tcells. As shown in FIG. 11A, a partial loss of activity was observedwhen the W residue at position 161 was removed; and a complete loss ofactivity was observed when the I residue at position 162 was removed.The deletion of a C-terminal L residue at position 167 also abolishedthe recognition of the peptide by TE4-2 T cells. Moreover, the residue Vat position 169 also appeared to be important, as deletion of thisresidue resulted in a two-fold decrease in the peptide's stimulatoryactivity. These results indicated that the W residue at position 161 maybe a P1 anchor, and the L residue at position 167 represented the P7anchor. The V residue at position 169 also appeared to contribute to thestimulatory capacity of the peptide epitope, indicating that it mayrepresent the P9 anchor residue. These putative anchor residues closelymatched the previously described consensus HLA DPB1*0401 binding motif(57).

The ESO p157-170 peptide, which contained all three anchor residues, wasused in the titration experiment to determine the minimal stimulatoryconcentration for the peptide. The results demonstrated that ESOp157-170 was able to stimulate significant cytokine releases from TE4-2T cells at a minimum concentration between 3 and 33 nM (FIG. 11B). Theseresults indicated that TE4-2 T cells recognized ESO p157-170 with a highaffinity. This apparent affinity is superior to most known MHC class IIbinding epitopes from non-mutated peptides, such as those from gp100(58), tyrosinase (59), and CDC-27 (54). Other peptides spanning the sameregion such as the ESO p161-180 and p156-175 also had similar minimalstimulatory concentrations for TE4-2 T cells (data not shown).

Interestingly, a previously identified HLA-A2 epitope, ESO p157-167 (47)was contained within the DPB1*0401-0402 epitope, ESO p157-170. To assesswhether the HLA-DP epitope may be presented by HLA-A2 and cross-reactwith CD8⁺ T cells, ESO p157-170 was tested for recognition by TE8-1, aCD8⁺ T cell line specifically recognizing the HLA-A2 epitope ESOp157-167. ESO p157-170 was able to stimulate significant cytokinereleases from TE8-1 T cells when pulsed onto L023 EBVB cells, whichexpressed HLA-A2 but not the DPB1*0401-0402 allele (FIG. 11C). Thisexperiment demonstrated that the ESO p157-170 epitope had dual MHC classI and class II specificity and could stimulate both CD4⁺ and CD8⁺ Tcells recognizing the NY-ESO-1 protein. Therefore, ESO p157-170 might bean attractive candidate for cancer vaccines aimed at eliciting both CD4⁺and CD8⁺ T cells specifically recognizing tumor cells.

Example 13 Association of the NY-ESO-1 Antibody Production with HLADPB1*0401-0402

HLA DPB1*0401-0402 is a dominant MHC class II allele present in a largeportion of Caucasians, ranging between 43% and 70% in population studiesinvolving different ethnic groups (52). Previous studies (48, 50) haveshown that normal donors as well as cancer patients without NY-ESO-1expressing tumors do not develop antibodies against NY-ESO-1. Incontrast, 50% of patients with NY-ESO-1 expressing tumors developedNY-ESO-1 specific Ab. In a panel of 88 melanoma patients whose serumsamples were tested, 11 patients were found to have high titers ofNY-ESO-1 antibodies (50). The previously identified DR4-restricted CD4⁺T cell peptides cannot account for the production of NY-ESO-1 specificAb since many patients did not express DR4 alleles at all (Table 2). Tofurther investigate whether NY-ESO-1 specific DP4-restricted CD4⁺ Tcells were associated with the production of NY-ESO-1 specific Ab inthese melanoma patients, we first analyzed their HLA DP subtypes. Tenout of the 11 patients with NY-ESO-1 antibodies expressed DPB1*0401and/or 0402, whereas no dominant DQ or DR restriction elements could beidentified in this group of patients (Table 2). Three patients from thispanel with known NY-ESO-1 expressing tumors but with no detectableantibodies did not express the DPB1*0401-0402 alleles. Since tumor celllines from the remaining 74 patients were not available to assess theNY-ESO-1 expression from these patients, further studies were notcarried out to identify their HLA DP types. A p-value of 0.011 wasobtained from a Fisher's exact test, indicating the significance of theassociation between antibody responses and the HLA-DPB1*0401-0402expression. Since NY-ESO-1 is expressed in 25-30% of tumor cell linesand DP4 is expressed in 43-70% of the population, the percentage ofpatients expressing both NY-ESO-1 and DP4 and with the potential todevelop antibody responses is in the range of 10-21%. This hypotheticalprediction is very close to the observed 10-13% frequency of patientswith NY-ESO-1 antibodies.

In order to obtain additional evidence as to the association betweenNY-ESO-1 antibody responses and the DPB1*0401-0402 expression, PBMC from6 of the 11 patients with NY-ESO-1 antibodies were used for in vitrostimulation with the ESO p161-180 peptide. In vitro sensitization wasalso carried out with PBMC from two DPB1*0401⁺ patients with nodetectable NY-ESO-1 antibodies. T cells were examined for their responseto 293CIITA cells pulsed with the ESO p161-180 peptide after two orthree rounds of in vitro stimulation. T cells from 5 out of the 6patients (including TE) with NY-ESO-1 antibodies showed a specificrecognition of the ESO p161-180 epitope presented by 293CIITA cells(DP4⁺ and HLA-A2⁻) (Table 3). Multiple wells from patient CT and BLappeared to react with peptide pulsed targets. Sensitized PBMC fromthese two patients also showed significant tumor recognition ofDPB1*0401⁺ and NY-ESO-1⁺ melanoma lines without further enrichment ofthe CD4⁺ T cells (data not shown). In contrast, NY-ESO-1 reactive Tcells were not generated using PBMC from two patients (WC and EW) withno detectable NY-ESO-1 antibodies after three stimulations. Theseresults suggested that patients who developed anti-NY-ESO-1 antibodiesalso contained relatively high precursor frequency of T cells reactivewith the DPB1*0401-restricted epitope. These NY-ESO-1 specific CD4⁺ Tcells may have contributed to the development of antibody responsesagainst the NY-ESO-1 cancer/testis antigen.

TABLE 3 Recognition of DPB1*0401-restricted ESO p161-180 by CD4⁺ T cellsgenerated from patients with and without specific antibody responses. TCell Reactivity (pg/ml IFN-gamma secretion) Antibody Patients Irrelevantpeptide^(@) ESO p161-180 Responses DPB1*0401 BE 0 0 + + FJ 0 160 + + CJ150 475 + + CT 150 2350 + + BL 180 1089 + + TE 90 207 + + WC^(%) 0 0 − +EW^(%) 0 0 − + ^(@)293CIITA cells (DPB1*0401 positive and HLA-A2negative) were pulsed with the indicated peptides and used as targets.Cultures showing more than 100 pg/ml IFN-production in response to ESOp161-180 pulsed targets and at least two-fold above the background weredefined as positive. Values of cytokine secretion were fromrepresentative positive wells. ^(%)Anti-NY-ESO-1 antibody titers as wellas the HLA DP types of patients WC and EW were determined in this study(data not shown). Expression of NY-ESO-1 in tumors from these twopatients was not known since their tumor specimens were not available.

Example 14

Modifications were made to one of the wild type HLA DP4 peptides. Themodification was designed to make the peptide more soluble so that itcould be purified to more than 90% homogeneity, which is required by FDAfor peptide clinical trials. The wild type as well as the modifiedpeptides are as follows:

Wild type ESOp157-170; (SEQ ID NO: 54) SLLMWITQCFLPVF;Wild type ESOp157-167; (SEQ ID NO: 79) SLLMWITQCFL; ESOp156R-169;(SEQ ID NO: 63) RSLLMWITQCFLPV; and ESOp157-170R; (SEQ ID NO: 64)SLLMWITQCFLPVR.

Experiments were carried out to test whether these modified peptideswere equality well recognized by T cells. Since ESO p157-170 showed dualHLA-A2 and HLA-DP4 binding specifications, the recognition in both DP4(FIG. 12A) and A2 (FIG. 12B) restricted fashion by TE4-2 CD4+ T cellsand TE8-1 CD8+ T cells, respectively was determined.

Results indicated that these modified peptides were equally wellrecognized as the wild type by CD4+ T cells as well as CD8+ T cells.

Example 15 NY-ESO-1 Epitope Specific CD4⁺ T Lymphocytes Immunotherapy

T-lymphocytes presensitized to a melanoma antigen may be effective intherapeutically treating mammals afflicted with a melanoma.T-lymphocytes are isolated from peripheral blood or melanoma tumorsuspensions and cultured in vitro (Kawakami, Y. et al, 1988, J. Exp.Med. 168:2183-2191).

The T lymphocytes are exposed to the epitope VLLKEFTVSG (SEQ ID NO: 19)or the epitope WITQCFLPVF (SEQ ID NO: 80) at a concentration of 1 μg/mlalone or in the presence of IL-2, resensitized and expanded in culture.CD4⁺ T-lymphocytes exposed to the epitope are administered to a mammalat about 10⁹ to 10¹² lymphocytes per mammal. The lymphocytes areadministered either intravenously, intraperitoneally or intralesionally.The treatment may be administered concurrently with other therapeutictreatments such as cytokines, surgical excision of melanoma lesions andchemotherapeutic drugs. NY-ESO-1 specific CD8⁺ T lymphocytes may beadministered concurrently with CD4⁺ T lymphocytes.

Example 16 Treatment of Patients with Metastatic Melanoma

In this protocol, patients with advanced melanoma are immunized with anantigenic cancer epitope.

Patients eligible for the trial must have evidence of measurable orevaluable metastatic melanoma that has failed standard effectivetherapy. Patients must have tumors that express the NY-ESO-1 antigen asevidenced by PCR or Northern Blot analysis of tumor cell RNA.

Patients receive either 1 ng, 1 μg, 1 mg or 500 mg/kg body weight of aMHC class II restricted T cell epitope via intravenously at day zero,day 7 and day 14 alone or in combination with IL2 and/or animmunostimulatory molecule. Patients are evaluated for toxicity,immunologic effects and therapeutic efficacy. Patients may additionallyreceive an NY-ESO-1 class I restricted T cell epitope.

Lymphocytes taken from the treated patients are tested for specificresponse to the NY-ESO-1 cancer antigen or MHC class II restricted Tcell epitope.

A complete response is defined as the disappearance of all clinicalevidence of disease that lasts at least four weeks. A partial responseis a 50% or greater decrease in the sum of the products of theperpendicular diameter of all measurable lesions for at least four weekswith no appearance of new lesions or increase in any lesions. Minorresponses are defined as 25-49% decrease in the sum of the products ofthe perpendicular diameters of all measurable lesions with no appearanceof new lesions and no increase in any lesions. Any patient with lessthan a partial response is considered a non-responder. The appearance ofnew lesions or greater than 25% increase in the product of perpendiculardiameters of prior lesions following a partial or complete response isconsidered as a relapse.

Discussion

NY-ESO-1 is an important immune target because it gives rise to bothhumoral and cellular immune responses (19-21). Although its expressionpattern is similar to antigens in the MAGE gene family, NY-ESO-1 is morefrequently expressed in breast, prostate and lung cancers than anymember of the MAGE family (19, 20, 23). More interestingly, high titeredNY-ESO-1 reactive antibodies were frequently detected in patients withcancer (FIGS. 2B and 2C) while a very low percentage of patientsdeveloped high titers of antibodies against the MAGE antigens ordifferentiation antigens such as tyrosinase, gp100, TRP-1 and TRP-2(data not shown and (22). These studies strongly suggest that NY-ESO-1reactive CD4⁺ T cells may be involved in antibody production and CTLproliferation. In this study, we identified the HLA-DR4-restricted Tcell epitope derived from NY-ESO-1 by the use of HLA-DR4-transgenic miceand in vitro stimulation of human PBMC with candidate peptides. To ourknowledge, this is the first demonstration that T cell epitopes fromNY-ESO-1 were shown to be presented by MHC class II molecules to CD4⁺ Tcells. Since NY-ESO-1-specific antibodies and CTL were detected inpatients with different HLA genotypes, other CD4⁺ T cell epitopespresented by HLA class II molecules other than HLA-DR4 were identifiedin the present invention.

Recently, two groups reported the identification of MHC classII-restricted T cell epitopes from the known MHC class I-restrictedtumor antigen, MAGE-3. CD4⁺ T cell clones generated from PBMC stimulatedwith DC pulsed with purified MAGE-3 protein recognized peptide orprotein pulsed on HLA-DR13-matched EBV B cells, but not MAGE-3⁺/DR13⁺tumor cells (14). However, in another study, CD4⁺ T cells generated fromPMBC stimulated with peptides predicted by a computer-assisted algorithmwere capable of recognizing both peptide pulsed on EBV B cells andMAGE-3⁻/DR11⁺ tumor cells (15). In the case of NY-ESO-1, we here showthat CD4⁺ T cells can recognize the NY-ESO-1 protein or peptide pulsedon DR4-matched EBV B cells as well as tumor cells expressing NY-ESO-1(FIGS. 4 and 5). Utilization of HLA-DR transgenic mice may haveadvantages in identifying putative peptides since immunized transgenicmice presumably have a high precursor frequency of specifically reactiveT cells. Once candidate peptides were identified, CD4⁺ T cells could begenerated from PBMC stimulated with synthetic candidate peptides.Therefore, the combined use of transgenic mice immunized with the wholeprotein and stimulated with the peptides predicted by acomputer-assisted algorithm may avoid the need to stimulate human PBMCwith a large number of peptides and several rounds of in vitrostimulation. Furthermore, candidate peptides identified by using theimmunized transgenic mice are likely to be peptides that are naturallyprocessed and presented on the cell surface. This may increase thelikelihood that peptide-specific CD4⁺ T cells can recognize tumor cellsas well. Finally, the use of PBMC from a patient (TE), who developed ahigh titer of antibody and a high precursor frequency of CTL againstNY-ESO-1, may make it easier to generate tumor-specific CD4⁺ T cellssince both antibody production and CTL require the help of CD4⁺ T cells.This approach has been used to identify a number of MHC classII-restricted T cell epitopes from known autoantigens involved inautoimmune diseases (28). Therefore, the strategy used in this study maybe applicable to many other known MHC class I-restricted tumor antigenswhile other strategies such as a direct gene cloning approach mayfacilitate the identification of unknown MHC class II-restricted tumorantigens.

Clinical trials using peptides derived from tissue-specificdifferentiation antigens such as gp100 showed some evidence oftherapeutic efficacy in the treatment of patients with melanoma (4).Although no significant toxic side effects were observed in the patientstreated with the modified gp100 peptides, vitiligo or depigmentation wasoften found in patients who responded to therapy (29), suggesting thatantitumor immunity induced by immunization with self-antigens may causeautoimmunity. In animal studies using TRP-1 as an immune target, similarresults (antitumor immunity and coat depigmentation) were also obtained(30-32). Interestingly, antitumor immunity and autoimmunity mediated bygp75/TRP-1 appeared to involve CD4⁺ T cells and antibodies (33).Immunization of mice with hTRP-2 (34), but not mTRP-2 (35), broketolerance to the self-antigen and the antitumor immunity required theparticipation of both CD4⁺ and CD8⁺ T cells (33). These studiessuggested that antitumor immunity could be mediated by either antibodiesor CD8⁺ T cells, but both require the critical help of CD4⁺ T cells (24,33).

The MHC class II-restricted NY-ESO-1 peptides identified in this studymay be useful in clinical applications since CTL and antibodies againstNY-ESO-1 were detected in patients with cancer. Immunization with bothMHC class I and II-restricted peptides or with a purified NY-ESO-1protein may induce NY-ESO-1 specific CD4⁺, CD8⁺ T cells as well asantibodies. Alternatively, patients could be immunized with dendriticcells loaded with both class I and II peptides or infected withrecombinant viruses encoding the NY-ESO-1 gene. Because testicular germcells do not express MHC class I and II molecules (36), immune responsesagainst NY-ESO-1 should be specific for tumor cells, and thus generatelittle or no autoimmune responses. Similar studies using MHC classI-restricted peptides of MAGE-3 or peptides pulsed on dendritic cellsindicated that while antitumor immunity (CTL responses) and slow tumorregression was demonstrated, no depigmentation/vitiligo or othersignificant side effects were observed (6, 7). Antitumor immunity may beenhanced by providing tumor-specific CD4⁺ T cell help.

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1-6. (canceled)
 7. An isolated nucleic acid comprising a nucleotidesequence encoding a peptide comprising Xaa₁ITQXaa₂FXaa₃PXaa₄ (SEQ ID NO:51) or a homolog thereof, wherein Xaa₁ Xaa₂, Xaa₃, and Xaa₄ are each atleast one amino acid residue and the peptide is immunologicallyrecognized by HLA-DP restricted CD4⁺ T lymphocytes.
 8. The nucleic acidof claim 7, wherein the peptide comprises an amino acid sequenceselected from the group consisting of SEQ ID NOs: 52-58 and 62-64.
 9. Arecombinant expression vector comprising the nucleic acid of claim 7.10. A host cell comprising the recombinant expression vector of claim 9.11. A recombinant virus comprising the nucleic acid of claim
 7. 12. Apharmaceutical composition comprising the nucleic acid of claim
 7. 13. Amethod of producing a recombinant HLA-DP restricted, CD4⁺ T cell epitopeof NY-ESO-1, the method comprising: (a) inserting the nucleic acid ofclaim 7 into an expression vector; (b) transferring the expressionvector into a host cell; (c) culturing the host cell under conditionssufficient for expression of the epitope or portion or homolog thereof;and (d) harvesting the recombinant epitope, or portion or homologthereof.
 14. A method of making a recombinant expression vectorcomprising incorporating the nucleic acid of claim 7 into a vector,wherein the nucleic acid sequence is operatively linked with a promoter.15. A method of detecting the presence of cancer or precancer in amammal, the method comprising: (a) contacting the nucleic acid of claim7 with a test biological sample of mRNA taken from the mammal, whereinthe contacting takes place under conditions sufficient to form a complexbetween the sequence and the mRNA; (b) detecting the complex; and (c)comparing the amount of mRNA in the test sample with an amount of mRNAfrom a known normal biological sample, wherein an increased amount ofmRNA in the test sample as compared to the known normal biologicalsample is indicative of cancer or precancer.
 16. A method of preventingor inhibiting cancer in a mammal, the method comprising administering tothe mammal the virus of claim 11 alone or in combination with anexogenous immunostimulatory molecule in an amount effective to preventor inhibit the cancer.
 17. A method of inhibiting growth of a tumorexpressing NY-ESO-1, the method comprising administering the nucleicacid of claim 7 in an amount effective to inhibit growth of the tumor.18. A pharmaceutical composition comprising the virus of claim 11 aloneor in combination with an exogenous immunostimulatory molecule,chemotherapy drug, antibiotic, antifungal drug, antiviral drug orcombination thereof and a pharmaceutically acceptable carrier.
 19. Anucleic acid vaccine construct comprising the nucleic acid of claim 7and at least one nucleotide sequence encoding a target antigen or targetepitope thereof.
 20. A method of inhibiting growth of cells expressingNY-ESO-1, the method comprising administering the virus of claim 11 inan amount effective to inhibit growth of the cells.
 21. A method ofinhibiting the growth of cells expressing NY-ESO-1, the methodcomprising administering the nucleic acid of claim 7 in an amounteffective to inhibit growth of the cells.
 22. An isolated nucleic acidwhich hybridizes under stringent conditions with the nucleic acid ofclaim
 7. 23. A pharmaceutical composition comprising the vectoraccording to claim 9 and a pharmaceutically acceptable carrier.